Dissertations / Theses on the topic 'Human Telomeric DNA'

Telomeres, the nucleoprotein structures at the ends of linear chromosomes, maintain genomic stability by protecting chromosome ends from fusion, degradation, and processing by the DNA double-strand break repair machinery. Telomere shortening, which occurs naturally in somatic cells during aging, leads to cellular senescence or apoptosis. In contrast, germline cells and cancer cells acquire unlimited replicative potential by activating a telomere lengthening mechanism, generally via reactivating the enzyme telomerase reverse transcriptase. To date, drug development targeting cellular immortalization in cancer has focused on telomerase inhibition. However, in a subset of tumours and in vitro-immortalized cell lines, telomeres are maintained by homologous recombination-mediated pathways, termed alternative lengthening of telomeres (ALT). ALT tumours are expected to be refractory to anti-telomerase therapies, so the ability to rapidly and reliably screen for ALT status in tumour-derived cells is essential for guiding therapeutic strategies that target cellular immortalization. One characteristic of ALT-mediated telomere maintenance is the presence of extrachromosomal telomeric repeat-containing DNA circles (t-circles), which provide an attractive target for detection in screening applications. Current methods oft-circle detection require considerable amounts of cells, making them unsuitable for analysis of limited clinical samples. We optimized a screen for ALT status based on a novel technique of rolling circle amplification (RCA) oft-circles from extrachromosomal DNA extracts of human ALT cells. We demonstrate that RCA requires a much lower number of cells than previously established t-circle detection methods, and screening many samples can be performed in parallel, making RCA suitable for analyzing clinical samples. T-circles were reproducibly detected in human immortalized ALT cell lines, but not in telomerase-utilizing cell lines. In addition, ectopic over-expression of telomerase in an ALT cell line does not appear to affect t-circle formation. This suggests that presence of active telomerase within a cell does not inhibit all telomeric recombination reactions. The potential for RCA as a tool to screen tumour samples for ALT activity and the link between telomerase and ALT-based telomere lengthening mechanisms are discussed.

The recent explosion of DNA sequence information has provided compelling evidence for the following facts. (1) Simple repetitive sequences-microsatellites and minisatellites occur commonly in the human genome and (2) these repetitive DNA sequences could play an important role in the regulation of various genetic processes including modulation of gene expression. These sequences exhibit extensive polymorphism in both length and the composition between species and between organisms of the same species and even cells of the same organism. The repetitive DNA sequences also exhibit structural polymorphism depending on the sequence composition. The functional significance of repetitive DNA is a well-established fact. The work done in many laboratories including ours has conclusively documented the functional role played by repetitive sequences in various cellular processes. Structural studies have established the sequence requirement for various non-B DNA structures and the functional significance of these unusual DNA structures is becoming increasingly clear. The structures that were characterised earlier purely from conformation point of view have aroused interest after the recent realisation that these structures could be formed in vivo when cloned in a supercoiled plasmid. The discovery of novel type of dynamic mutations where intragenic amplifications of trinucleotide repeats is associated with phenotypic changes causing many neurodegenerative disorders has provided the most compelling evidence for the importance of simple repeats in the etiology of these disorders. Secondary structures adopted by these simple repeats is a common causative factor in the mechanism of expansion of these repeats. This realisation prompted many investigations into the relationship between the DNA sequence, structure and molecular basis of dynamic mutation. Many experimental evidences have implicated paranemic DNA structures in various biological processes, especially in the regulation of gene expression. Earlier work done in our laboratory on the structure function relationship of repetitive DNA sequences provided experimental evidence for the role of paranemic DNA structure in the regulation of gene expression. It was demonstrated that intramolecular triplex potential sequences within a gene downregulate its expression in vivo (Sarkar and Brahmachari (1992) Nucleic Acids Res., 20, 5713-5718). Similarly the effect of cruciform structure forming sequences on gene expression was also documented. Sequence specific alterations in DNA structures were studied in our laboratory using a variety of biophysical and biochemical techniques. An intramolecular, antiparallel tetraplex structure was proposed for human telomeric repeat sequences (Balagurumoorthy, et al., (1994) J. Biol. Chem., 269, 21858-21869). The telomeric repeats are not only present at the end of chromosomes but they are also present at many interstitial sites in the human genome. Database search reveals that the human telomeric sequences as well as similar sequences with minor variations are present at many locations in the human genome. Telomeric repeats are GC rich sequences with the G rich strand protruding as a 3' end overhang at the end of chromosomes. When human telomeric repeats are cloned in a supercoiled plasmid, the C rich strand adopts a hairpin like conformation where as the G-rich strand extrudes into a quadruplex structure. However, the biological significance of these structures in vivo still remains to be elucidated completely. The role of a putative tetraplex DNA structure in the insulin gene linked polymorphic region of the human insulin gene in vivo in the regulation of expression of the insulin gene has been suggested. In this context, we have addressed the question whether the telomeric repeats when present within a gene affect its expression in vivol If so, what would be the possible mechanism? An attempt has been made to understand the effect of presence of telomeric repeats within a gene on its expression. The details of these studies have been presented in Chapter 2 of this thesis. Contrary to telomeric repeats which provide stability to the chromosomes, recently expansion of a GC rich dodecamer repeat upstream of cystatin B gene (chromosome 21q) has been shown to be the most common mutation associated with Progressive Myoclonus Epilepsy (EPM1) of Unverricht-Lundberg type. Two to three copies of the repeat (CCCCGCCCCGCG)n are present in normal individuals whereas the affected individuals have 30-75 copies of this repeat. The expression of cystatin B gene is reduced in patients in a cell specific manner. The repeat also shows intergenerational variability. The exact mechanism of expansion of this repeat is not known. In the case of trinucleotide repeat expansion, it is shown that the structure adopted by the repeat plays an important role in the mechanism of expansion and that some of the secondary structures adopted by trinucleotide repeats could be inherently mutagenic conformations. In order to understand the mechanism of expansion EPM1 dodecamer repeat, the work reported in this thesis was carried out with the following objectives. • To understand the structure of G rich and C-rich strands of EPM1 repeat. • To understand the variations in the structure with the increase in the length and its possible implications in the mechanism of expansion of EPM 1 repeat. Studies aimed with these objectives are presented in chapters 3, 4 and 5 of the thesis. Chapter 1 provides a general introduction to repetitive DNA, the various structures adopted by repetitive DNA sequences in the genome, the functional significance of the various simple repetitive DNA sequences in the genome has been presented. An account of trinucleotide repeat expansion and associated disorders, non-trinucleotide repeat expansions and associated disorders has been presented. The various non B-DNA structures adopted these repeats and their implications in the mechanism of expansion have been discussed. Chapter 2 describes in frame cloning of human telomeric repeats d(G3T2A)3G3 in the N-terminal region of β-galactosidase gene. The effect of such repeat Sequences on transcription elongation in vivo has been studied using E.coli as a model system. The 3.5 copies of human telomeric repeat sequences were cloned in the sense strand of plasmid pBluescriptllSK+ so as to create plasmid clone pSBQ8 and in the template strand of plasmid pBluescriptHKS+ so as to create clone pSBRQ8. One dimensional chloroquine gel shift assay indicated presence of an unwound structure in pSBQ8 and pSBRQ8. β-galactosidase activity assay suggested downregulation of the gene in vivo. In the case of plasmid pSBQ8 the difference in β-galactosidase activity was approximately 6 fold as compared to the parent plasmid pBluescriptIISK+ whereas in the case of pSBRQ8 the difference in β-galactosidase activity was approximately 8 fold as compared to the control pBluescriptIIKS+. The analysis of β-galactosidase transcript showed that full length transcript was formed in the case of pSBQ8. Full length transcript was not formed in the case of pSBRQ8. We propose that in the case of pSBQ8 the gene expression is inhibited in steps subsequent to transcription elongation. In the case of pSBRQ8, we propose that quadruplex structure may be formed by the template strand at the DNA level thereby blocking transcription elongation step. Chapter 3 describes studies aimed at understanding the structure of G-rich strand (referred to as G strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the G strand of dodecamer EPM1 repeat is d(GGGGCGGGGCGC)n. Oligoucleotides containing one (12mer), two (24mer) and three(36mer) were synthesised. These oligonucleotides are referred to as dG12, dG24 and dG36 respectively. Structural studies were carried out using CD spectroscopy, UV melting, non-denaturing gel electrophoresis and chemical and enzymatic probing. The G strand oligonucleotides showed enhanced gel elecrophoretic mobility in the presence of monovalent cations KCl and NaCl. Oligonucleotide dG12 also showed retarded species on non-denaturing gel in the presence of 70mM KCl indicating intermolecular associations. Oligonucleotides dG24 and dG36 predominantly formed intramolecular structures which migrated anomalously faster than the expected size. The CD spectrum for dG12 showed an intense positive band at 260nm and a negative band at 240nm in the presence of KCl indicative of an intermolecular, parallel G quartet structure. The CD spectra of dG24 and dG36 showed 260nm positive peak, 240nm negative peak along with a positive band around 290nm. This is indicative of folded back structure. These findings support the results of non-denaturing gel electrophoresis of G strand oligonucleotides. The UV melting profiles suggested increase in the stability with the increase in the length. These structures were further characterised by PI nuclease and chemical probing using DMS and DEPC. The structural studies with G-rich strand of EPM1 dodecamer repeat showed that this repeat motif adopts intramolecularly folded structures with increase in the length of the repeat thereby favouring slippage during replication. Chapter 4 deals with the studies aimed at understanding the structure at acidic pH of C-rich strand (referred to as C strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the C strand of dodecamer EPM1 repeat is d(CCCCGCCCCGCG)n. The C rich oligonucleotides are known to form a four stranded structure called i-motif at acidic pH involving intercalated base pairs. The i-motif consists of two parallel stranded, base paired duplexes are arranged in an antiparallel orientation. Since, the base pairs of one base paired duplex intercalate into those of the other duplex, the structure is called as i-motif. We have investigated structure of C strand of EPM1 repeat by circular dichroism (CD), native polyacrylamide gel electrophoresis and UV melting. Oligonucleotide dC12 showed two bands of which the major band was retarded on the native gel (pH 5.0) at low temperature suggesting that dC12 predominantly formed intermolecular structure, Oligonucleotides dC24 and dC36 migrated anomalously faster than the expected size indicating formation of compact, intramolecularly folded structures. Circular dichroism studies indicate that, all the oligonucleotides displayed an intense positive band near 285nm, a negative band around 260nm with a cross over at 270nm, This is a characteristic CD signature for an i-motif structure and reflects the presence of secondary structure due to formation of hydrogen bonded pairs between protonated cytosines. All the C strand oligonucleotides showed hyperchromism at 265nm, which is an isobestic wavelength for C protonation. Studies described in this chapter suggest an intramolecular i-motif structure for dC24 and dC36 and an intermolecular i-motif for oligonucleotide dC12. In addition, it was interesting to note that inspite of the presence of G residues, the stretch of C residues could adopt i-motif structure. Although these structures are formed at an acidic pH, it is indicative of formation of possible intramolecularly folded structure. Many reports have suggested the possibility of cytosine rich sequences adopting i-motif structure even at neutral pH. In order to test this possibility, structural studies were carried out on the C strand EPM1 oligonucleotides at pH 7.2 in the presence of 70mM NaCl. These studies have been described in Chapter 5. The investigations were done using CD spectroscopy, UV melting, native polyacrylamide gel electrophoresis, and chemical probing using hydroxylamine and PI nuclease. These studies indicate that all the C strand oligonucleotides form intramolecular, hairpin structure at physiological pH. All the three C strand oligonucleotides migrated anomalously faster on the native gel indicating the presence of a compact structure. The CD spectra at pH 7.2 showed a blue shift as compared to those at pH 5.0. This indicated absence of base pairs. The hydroxylamine chemical probing suggested presence of G-C Watson-Crick base pairs. The loop residues of the folded back hairpin structures were probed with PI nuclease. The C strand oligonucleotides showed possibility of formation of multiple hairpin structures with the increase in the length of the repeat. The propensity to form hairpin structures suggests a possibility of formation of slip loop structures during the replication process thereby promoting expansion of this repeat. Formation of folded back hairpin like structures is significant in terms of mechanism of expansion of this repeat. Chapter 6 is devoted to concluding remarks highlighting the significance of the experimental results presented in this thesis and their possible biological implications in the light of contemporary research.

The recent explosion of DNA sequence information has provided compelling evidence for the following facts. (1) Simple repetitive sequences-microsatellites and minisatellites occur commonly in the human genome and (2) these repetitive DNA sequences could play an important role in the regulation of various genetic processes including modulation of gene expression. These sequences exhibit extensive polymorphism in both length and the composition between species and between organisms of the same species and even cells of the same organism. The repetitive DNA sequences also exhibit structural polymorphism depending on the sequence composition. The functional significance of repetitive DNA is a well-established fact. The work done in many laboratories including ours has conclusively documented the functional role played by repetitive sequences in various cellular processes. Structural studies have established the sequence requirement for various non-B DNA structures and the functional significance of these unusual DNA structures is becoming increasingly clear. The structures that were characterised earlier purely from conformation point of view have aroused interest after the recent realisation that these structures could be formed in vivo when cloned in a supercoiled plasmid. The discovery of novel type of dynamic mutations where intragenic amplifications of trinucleotide repeats is associated with phenotypic changes causing many neurodegenerative disorders has provided the most compelling evidence for the importance of simple repeats in the etiology of these disorders. Secondary structures adopted by these simple repeats is a common causative factor in the mechanism of expansion of these repeats. This realisation prompted many investigations into the relationship between the DNA sequence, structure and molecular basis of dynamic mutation. Many experimental evidences have implicated paranemic DNA structures in various biological processes, especially in the regulation of gene expression. Earlier work done in our laboratory on the structure function relationship of repetitive DNA sequences provided experimental evidence for the role of paranemic DNA structure in the regulation of gene expression. It was demonstrated that intramolecular triplex potential sequences within a gene downregulate its expression in vivo (Sarkar and Brahmachari (1992) Nucleic Acids Res., 20, 5713-5718). Similarly the effect of cruciform structure forming sequences on gene expression was also documented. Sequence specific alterations in DNA structures were studied in our laboratory using a variety of biophysical and biochemical techniques. An intramolecular, antiparallel tetraplex structure was proposed for human telomeric repeat sequences (Balagurumoorthy, et al., (1994) J. Biol. Chem., 269, 21858-21869). The telomeric repeats are not only present at the end of chromosomes but they are also present at many interstitial sites in the human genome. Database search reveals that the human telomeric sequences as well as similar sequences with minor variations are present at many locations in the human genome. Telomeric repeats are GC rich sequences with the G rich strand protruding as a 3' end overhang at the end of chromosomes. When human telomeric repeats are cloned in a supercoiled plasmid, the C rich strand adopts a hairpin like conformation where as the G-rich strand extrudes into a quadruplex structure. However, the biological significance of these structures in vivo still remains to be elucidated completely. The role of a putative tetraplex DNA structure in the insulin gene linked polymorphic region of the human insulin gene in vivo in the regulation of expression of the insulin gene has been suggested. In this context, we have addressed the question whether the telomeric repeats when present within a gene affect its expression in vivol If so, what would be the possible mechanism? An attempt has been made to understand the effect of presence of telomeric repeats within a gene on its expression. The details of these studies have been presented in Chapter 2 of this thesis. Contrary to telomeric repeats which provide stability to the chromosomes, recently expansion of a GC rich dodecamer repeat upstream of cystatin B gene (chromosome 21q) has been shown to be the most common mutation associated with Progressive Myoclonus Epilepsy (EPM1) of Unverricht-Lundberg type. Two to three copies of the repeat (CCCCGCCCCGCG)n are present in normal individuals whereas the affected individuals have 30-75 copies of this repeat. The expression of cystatin B gene is reduced in patients in a cell specific manner. The repeat also shows intergenerational variability. The exact mechanism of expansion of this repeat is not known. In the case of trinucleotide repeat expansion, it is shown that the structure adopted by the repeat plays an important role in the mechanism of expansion and that some of the secondary structures adopted by trinucleotide repeats could be inherently mutagenic conformations. In order to understand the mechanism of expansion EPM1 dodecamer repeat, the work reported in this thesis was carried out with the following objectives. • To understand the structure of G rich and C-rich strands of EPM1 repeat. • To understand the variations in the structure with the increase in the length and its possible implications in the mechanism of expansion of EPM 1 repeat. Studies aimed with these objectives are presented in chapters 3, 4 and 5 of the thesis. Chapter 1 provides a general introduction to repetitive DNA, the various structures adopted by repetitive DNA sequences in the genome, the functional significance of the various simple repetitive DNA sequences in the genome has been presented. An account of trinucleotide repeat expansion and associated disorders, non-trinucleotide repeat expansions and associated disorders has been presented. The various non B-DNA structures adopted these repeats and their implications in the mechanism of expansion have been discussed. Chapter 2 describes in frame cloning of human telomeric repeats d(G3T2A)3G3 in the N-terminal region of β-galactosidase gene. The effect of such repeat Sequences on transcription elongation in vivo has been studied using E.coli as a model system. The 3.5 copies of human telomeric repeat sequences were cloned in the sense strand of plasmid pBluescriptllSK+ so as to create plasmid clone pSBQ8 and in the template strand of plasmid pBluescriptHKS+ so as to create clone pSBRQ8. One dimensional chloroquine gel shift assay indicated presence of an unwound structure in pSBQ8 and pSBRQ8. β-galactosidase activity assay suggested downregulation of the gene in vivo. In the case of plasmid pSBQ8 the difference in β-galactosidase activity was approximately 6 fold as compared to the parent plasmid pBluescriptIISK+ whereas in the case of pSBRQ8 the difference in β-galactosidase activity was approximately 8 fold as compared to the control pBluescriptIIKS+. The analysis of β-galactosidase transcript showed that full length transcript was formed in the case of pSBQ8. Full length transcript was not formed in the case of pSBRQ8. We propose that in the case of pSBQ8 the gene expression is inhibited in steps subsequent to transcription elongation. In the case of pSBRQ8, we propose that quadruplex structure may be formed by the template strand at the DNA level thereby blocking transcription elongation step. Chapter 3 describes studies aimed at understanding the structure of G-rich strand (referred to as G strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the G strand of dodecamer EPM1 repeat is d(GGGGCGGGGCGC)n. Oligoucleotides containing one (12mer), two (24mer) and three(36mer) were synthesised. These oligonucleotides are referred to as dG12, dG24 and dG36 respectively. Structural studies were carried out using CD spectroscopy, UV melting, non-denaturing gel electrophoresis and chemical and enzymatic probing. The G strand oligonucleotides showed enhanced gel elecrophoretic mobility in the presence of monovalent cations KCl and NaCl. Oligonucleotide dG12 also showed retarded species on non-denaturing gel in the presence of 70mM KCl indicating intermolecular associations. Oligonucleotides dG24 and dG36 predominantly formed intramolecular structures which migrated anomalously faster than the expected size. The CD spectrum for dG12 showed an intense positive band at 260nm and a negative band at 240nm in the presence of KCl indicative of an intermolecular, parallel G quartet structure. The CD spectra of dG24 and dG36 showed 260nm positive peak, 240nm negative peak along with a positive band around 290nm. This is indicative of folded back structure. These findings support the results of non-denaturing gel electrophoresis of G strand oligonucleotides. The UV melting profiles suggested increase in the stability with the increase in the length. These structures were further characterised by PI nuclease and chemical probing using DMS and DEPC. The structural studies with G-rich strand of EPM1 dodecamer repeat showed that this repeat motif adopts intramolecularly folded structures with increase in the length of the repeat thereby favouring slippage during replication. Chapter 4 deals with the studies aimed at understanding the structure at acidic pH of C-rich strand (referred to as C strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the C strand of dodecamer EPM1 repeat is d(CCCCGCCCCGCG)n. The C rich oligonucleotides are known to form a four stranded structure called i-motif at acidic pH involving intercalated base pairs. The i-motif consists of two parallel stranded, base paired duplexes are arranged in an antiparallel orientation. Since, the base pairs of one base paired duplex intercalate into those of the other duplex, the structure is called as i-motif. We have investigated structure of C strand of EPM1 repeat by circular dichroism (CD), native polyacrylamide gel electrophoresis and UV melting. Oligonucleotide dC12 showed two bands of which the major band was retarded on the native gel (pH 5.0) at low temperature suggesting that dC12 predominantly formed intermolecular structure, Oligonucleotides dC24 and dC36 migrated anomalously faster than the expected size indicating formation of compact, intramolecularly folded structures. Circular dichroism studies indicate that, all the oligonucleotides displayed an intense positive band near 285nm, a negative band around 260nm with a cross over at 270nm, This is a characteristic CD signature for an i-motif structure and reflects the presence of secondary structure due to formation of hydrogen bonded pairs between protonated cytosines. All the C strand oligonucleotides showed hyperchromism at 265nm, which is an isobestic wavelength for C protonation. Studies described in this chapter suggest an intramolecular i-motif structure for dC24 and dC36 and an intermolecular i-motif for oligonucleotide dC12. In addition, it was interesting to note that inspite of the presence of G residues, the stretch of C residues could adopt i-motif structure. Although these structures are formed at an acidic pH, it is indicative of formation of possible intramolecularly folded structure. Many reports have suggested the possibility of cytosine rich sequences adopting i-motif structure even at neutral pH. In order to test this possibility, structural studies were carried out on the C strand EPM1 oligonucleotides at pH 7.2 in the presence of 70mM NaCl. These studies have been described in Chapter 5. The investigations were done using CD spectroscopy, UV melting, native polyacrylamide gel electrophoresis, and chemical probing using hydroxylamine and PI nuclease. These studies indicate that all the C strand oligonucleotides form intramolecular, hairpin structure at physiological pH. All the three C strand oligonucleotides migrated anomalously faster on the native gel indicating the presence of a compact structure. The CD spectra at pH 7.2 showed a blue shift as compared to those at pH 5.0. This indicated absence of base pairs. The hydroxylamine chemical probing suggested presence of G-C Watson-Crick base pairs. The loop residues of the folded back hairpin structures were probed with PI nuclease. The C strand oligonucleotides showed possibility of formation of multiple hairpin structures with the increase in the length of the repeat. The propensity to form hairpin structures suggests a possibility of formation of slip loop structures during the replication process thereby promoting expansion of this repeat. Formation of folded back hairpin like structures is significant in terms of mechanism of expansion of this repeat. Chapter 6 is devoted to concluding remarks highlighting the significance of the experimental results presented in this thesis and their possible biological implications in the light of contemporary research.

Telomeres are physical ends of chromosomes consisting of (TTAGGG)n DNA sequence and a specialized set of proteins that protect chromosomal ends from degradation and from eliciting DNA damage response. These specialized set of proteins, known as shelterin, directly bind to telomeric DNA. In addition, some DNA double-strand break (DSB) repair proteins such as, DNA-PKcs and KU70/80, play active roles in telomere maintenance. Mouse knock-out experiments have revealed that deletion of either DNA-PKcs or Ku70/80 resulted in elevated levels of telomeric fusion, indicative of dysfunctional telomeres. Artemis protein is involved in DNA DSB repair through non-homologous end joining (NHEJ) and it is phosphorylated by DNAPKcs. Human cells defective in Artemis have been identified and shown to be radiosensitive and patients with an Artemis defective gene suffer from radiosensitive severe-combined immune deficiency syndrome (RS-SCID). Mouse cells defective in Artemis have elevated levels of telomeric fusion. We have demonstrated in this thesis that Artemis defective human cell lines show a mild telomeric dysfunction phenotype detectable at the cytological level. The nature of telomere dysfunction phenotype appears to be similar to that observed in DNAPKcs defective cells as exemplified by the presence of IR induced chromatid telomeric fusions. We have also shown that (a) DNA damage occurring within the telomeric DNA is difficult to repair or irreparable in older cells and that (b) Artemis defective older cells show higher proportion of DNA damage at telomeres than their normal counterparts. Finally, we have demonstrated that inhibition of DNA-PKcs causes (a) an increase in telomeric fusions in Artemis defective cell lines relative to both normal cell lines after inhibition and Artemis cell lines before inhibition and (b)elevated levels of DNA damage at telomeres following exposure of cells to radiation relative to both irradiated normal cells exposed to a DNA-PKcs inhibitor and irradiated Artemis defective cells but not exposed to the DNA-PKcs inhibitor. These results suggest that the effects of Artemis and DNA-PKcs on telomeres are cumulative. We have also performed (a) experiments to examine telomere function in Artemis defective cell lines after knocking down DNA-PKcs levels by RNAi and b) preliminary experiments to knock-down Artemis in DNA-PKcs defective cells. Taken together, our results suggest that the Artemis defect causes mild telomere dysfunction phenotype in human cells.

Telomere shortening is a major mechanism to induce telomere uncapping and thus to signal growth arrest and/ or apoptosis and can be caused by different mechanisms, one of which is damage to DNA, to which telomeres appear to be particularly sensitive. Contradictory data exists on the relationship between conventionally used chemotherapeutic drugs and the telomere/ telomerase complex. The aim of the work described in this thesis was to determine whether or not damage to telomeres played a significant role in the cytotoxic action of the anti-cancer drugs cisplatin and etoposide. Two cell lines were used with either short (neuroblastorna cell line SHSY5Y) or long (lymphoblastic T cell line 1301) telomeres. Cytotoxic effects of the drugs were assessed by growth inhibition assays and measurement of apoptosis and cell cycle progression by flow cytometry. Etoposide caused readily detectable DNA strand breakage and led to formation of nuclear foci of phosphorylated histone y-H2A. X. Cisplatin treatment did not induce strand breaks after initial drug exposure but strand breaks and DNA damage foci were detected after further incubation. For cells with either long or short telomeres, no detectable changes in total telomere length or overhang length were observed before apoptosis became manifest. Preferential occurrences of single strand breaks in the G-rich strand of telorneres were not found. Through the development of a dual staining method it was established that drug-induced histone H2A. X foci did not colocalise to the telomeres. Telomerase was transiently activated by lower concentrations of etoposide and its activity decreased only after onset of apoptosis. Taken together, the results show no indication that telorneres and/ or telomeric damage play any preferential role as signal transducers towards apoptosis and/ or growth arrest in either of these cell lines. Also, the protective function of telornerase &-I - seems to be telomere independent. The data are consistent with a model of druginduced growth arrest and apoptosis being triggered by damage elsewhere in the genome.

G-quadruplex structures are found in important regions of the eukaryotic genome, such as telomeres and regulatory sequences of genes, and are likely to play important roles in regulation of biological events. The significant structural differences with duplex DNA make quadruplex DNA a very attractive target for anticancer drug design. The purpose of this study is to explore conformational space in a series of heterocyclic cations to discover novel structural motifs that can selectively bind and stabilize specific G-quadruplex arrangements. A variety of biophysical techniques such as thermal melting experiments, biosensor surface plasmon resonance, circular dichroism, fluorescence displacement assay and mass spectrometry were employed to evaluate the affinity of the compounds and their recognition properties. The screening of the molecules allowed the identification of not only selective G-quadruplex ligands but also potential quadruplex groove binders. These results can be useful for the development of new efficient telomerase inhibitors which are endowed with pharmacological activity.

G-quadruplex forming human telomere sequence (HTS) DNA, has been widely studied due to the telomere's implied role in biological processes, including cellular ageing and cancer physiology. The goal of these previous efforts has been to characterize the physiologically relevant structures and their stability and dynamics in order to develop therapeutic applications. Unfortunately, understanding the biologically relevant form of the human telomere DNA is complicated by the fact that HTS-derived sequences are highly polymorphic. To further complicate the issue, recent investigations have demonstrated the ability of "cell-like" co-solvents to alter the preferred G-quadruplex fold of HTS DNA. However, the origins of G-quadruplex structure selection, the relative contributions of crowding versus dehydration, and the possible effects of co-solvents on kinetically determined folding pathways remain unresolved. Towards answering these questions, I investigated HTS DNA G-quadruplex in extreme anhydrous and high viscosity conditions utilizing a deep eutectic solvent (DES) consisting of choline chloride and urea. Herein I report that the water-free DES supports an extremely stable parallel stranded structure, consistent with observations that diminished water activity is the main cause of structural transitions to the "parallel-propeller" form. Furthermore, my research shows that the highly viscous nature of the solvent enables significant diffusion based control over HTS g-quadruplex folding rates and topology, fully consistent with Kramers rate theory. To the best of my knowledge, this is the first example of the kinetic exploration of G-quadruplex folding utilizing high friction solvent; the results of which display a decreased intramolecular folding rate of HTS DNA to a never before encountered time scale on the order of days at physiological temperature. Moreover, I have demonstrated that the folding pathway of a G-quadruplex can be altered with increased solvent friction. These discoveries are important because they highlight the need to consider the viscosity when exploring the dynamics of human telomeres specifically drug binding and folding of G-quadruplexes in vivo where cellular viscosity has been reported to be as high as 140cP. Lastly, it appears that tuning solvent viscosity could prove useful to the continued study of G-quadruplex dynamics.

Le matériel génétique contenant l'information des cellules humaines se présente sous forme de chromosomes linéaires dont l'extrémité est protégée par une structure appelée télomères. Les télomères correspondent à une séquence d'ADN répétée, recouverte de protéines spécifiques, qui permettent aux cellules d'étiqueter l'extrémité de leurs chromosomes afin de les différencier des cassures internes de l'ADN nécessitant une réparation. Ainsi, ils jouent un rôle prépondérant dans la protection du génome. Les chromosomes sont organisés et compartimentés dans le noyau de la cellule. Cette organisation est primordiale, la proximité des chromosomes à la membrane nucléaire qui délimite ce noyau est essentielle pour de nombreuses fonctions régulatrices du génome, comme l'activation et la répression des gènes contenant les informations. A chaque division cellulaire, cette organisation est perdue après le désassemblage de la membrane nucléaire et la condensation de la chromatine qui va permettre de correctement répartir les chromosomes entre les cellules filles. Après la division, les noyaux des cellules filles se reforment, la membrane nucléaire est rétablie, et les chromosomes sont repositionnés comme dans la cellule mère. Ce mécanisme de mémoire spatiale est encore inconnu mais est vital au maintien de la stabilité du génome. Une large proportion de télomères sont ancrés à la membrane nucléaire en fin de division, et y restent durant la reformation du noyau. Le laboratoire s'intéresse à cette association afin de caractériser son rôle pendant cette phase clé du cycle cellulaire. Nous cherchons à comprendre ce fonctionnement chez les cellules normales et les cellules de patients atteints de pathologies associées au vieillissement accéléré. Ce projet de thèse à pour but de comprendre l'impact d'une déformation de la membrane nucléaire sur le matériel génétique, et sur l'intégrité des télomères qui protègent l'information génétique. Nous utilisons des techniques de pointe de microscopie, et de biologie cellulaire et moléculaire afin de mieux comprendre le lien entre l'organisation du noyau et le maintien de la stabilité du génome
The material that contains genetic information of human cells consists in linear chromosomes. The extremities of chromosomes are protected by a specific structure called telomeres. Telomeres are made of repeated DNA sequence, covered by special proteins that prevent cells to recognize extremities of their chromosomes as internal DNA break, thus not to perform unnecessary repair that will result in genome instability. Therefore, telomeres play a major role in genome protection. Chromosomes are spatially organized in the cell nucleus. This organization is important as positioning of chromosomes in the nucleus ensures proper regulatory functions of the genome, such as activation or repression of genes. During the cell division process, this organization is lost after nuclear membrane disassembly and the condensation of DNA, to allow correct segregation of chromosomes between daughter cells. After cell division, the nuclei of daughter cells are reformed, and nuclear membrane is reconstructed. The chromosomes are then relocated as in the mother cell. This mechanism of spatial memory is not well understood yet, but is key to maintain stability of the genome. A large proportion of telomeres are anchored to the nuclear membrane at the end of mitosis, and stay during nuclear envelope reformation. Our laboratory focuses on characterizing the role of telomere anchoring during this important phase of cell cycle. In particular, we want to understand this mechanism in normal cells and cells from patients with premature aging disease. This thesis aims to understand the impact of nuclear envelope abnormalities on the genetic material, in particular on telomere integrity, as telomeres protect genetic information. Here, we use microscopy approaches and techniques of molecular and cellular biology to better understand the link between nuclear organisation and genome stability maintenance

Telomere dysfunction is one mechanism of cellular and tissue ageing. Dysfunctional telomeres in fibroblasts are recognised as DNA double-strand breaks (DSBs) and trigger the DNA damage pathway of senescence. However, telomere uncapping in normal human epidermal keratinocytes, via expression of the dominant negative mutant of the telomere repeat-binding factor 2 (TRF2!B!M), resulted in a senescent-like arrest without a significant DNA damage response (DDR). This suggests that either keratinocytes are unusually sensitive to telomere uncapping and the low DDR is sufficient to induce senescence or that dysfunctional telomeres may also be signalled through an alternative pathway. Subsequent analysis revealed genes HIST2H2BE, ICEBERG, S100A7 and HOPX as potential markers for telomere dysfunction-induced senescence (TDIS) since they were induced by telomere uncapping and seemed to be regulated by telomerase. The aim of this project was to assess the specificity of these candidate markers for TDIS and to select the most promising for use as a biomarker. To this end, keratinocytes were exposed to doses of ionising radiation, capable of generating transient or permanent damage to the DNA, or transduced with retroviral constructs expressing p14ARF, p16INK4a, p53 or TRF2!B!M and the gene expression levels of the candidates assessed after a recovery period or at the early stages of senescence. Whilst S100A7, HOPX or ICEBERG were not induced by a transient or persistent DDR or by p16INK4a, ICEBERG and HOPX were induced by p53 and p14ARF when these were ectopically expressed at higher levels. Thus, S100A7 seems to be the most specific early marker for telomere dysfunction in keratinocytes since it was selectively induced by telomere uncapping via expression of TRF2!B!M and not by DSBs or by over expression of p14ARF, p53 or p16INK4a. S100A7 may have the potential to identify cells with telomere dysfunction in human epithelia and body fluids.

Thesis (Ph.D.)--Boston University
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It has been demonstrated that oligonucleotides homologous to the 3' telomere repeat sequence TTAGGG (T-oligos) stimulate DNA damage responses that are also induced by disruption of the telomere loop structure. Adaptive defense against oxidative stress and UV or ionizing radiation has been reported, but adaptive antioxidant defense as a response to mimicking telomere loop exposure has not been described. The T-oligos pTT and pGTTAGGGTTAG were added to human dermal fibroblast cultures to investigate whether mimicking telomere loop disruption stimulates antioxidant defense. pTT stimulated mitochondrial superoxide dismutase protein levels within 72 hours. Cell yields were higher after H202 exposure in fibroblasts pretreated with pTT for 72 hours compared to diluent pretreated cells. Intracellular reactive oxygen species (ROS) levels, measured by flow cytometry and the dichlorofluorescein diacetate probe, increased during T-oligo treatment as compared to diluent and oligonucleotide controls. The time course and degree of ROS stimulation corresponded to the time course for activation and/or induction of p53 and p21/Cip1/Waf1. The NADPH oxidase inhibitor diphenyliodonium chloride abrogated this increase and fibroblasts retrovirally transduced to produce dominant negative p53 failed to display increased ROS, implicating that the T-oligos induced ROS through p53-responsive NADPH oxidases. A horseradish peroxidase assay for extracellular H20 2 showed no H20 2 release with pTT treatment. To determine whether there was induction of senescence, an endpoint response to increased ROS and prolonged T-oligo treatment in fibroblasts, the senescence-associated β-galactosidase assay was conducted in parallel with the DCF assay. Only the 11mer T-oligo treatment modestly increased the number of β-galactosidase positive cells by 72 hours (<30% of cells). This is the first report suggesting that antioxidant defense and ROS signaling are part of the broad adaptive response in mammalian cells presumably initiated by telomere loop disruption and mimicked by T-oligos. T-oligo treatment thus offers a new model for studies of ROS signaling in human dermal fibroblasts, allowing exploration of the relationships between DNA damage, ROS, oxidative stress, and the evolution of cellular defense mechanisms.
2031-01-01

Telomeres are nucleoprotein complexes located at the end of chromosomes. They have an essential role in protecting chromosome ends. Telomerase or ALT (alternative lengthening of telomeres) mechanisms maintain telomeres by compensating natural telomeric loss. We have set up a flow-FISH method and using mouse lymphoma cell lines we identified unexpectedly the presence of subpopulations of cells with different telomere lengths. Subpopulations of cells with different telomere lengths were also observed in a human ALT and non-ALT cell line. Differences in telomere length between subpopulations of cells were significant and we term this phenomenon TELEFLUCS (TElomere LEngth FLUctuations in Cell Subpopulations). By applying flow-FISH we could successfully measure telomere lengths during replicative senescence in human primary fibroblasts with different genetic defects that confer sensitivity to ionising radiation (IR). The results from this study, based on flow-FISH and Southern hybridisation measurements, revealed an accelerated rate of telomere shortening in radiosensitive fibroblasts. We also observed accelerated telomere shortening in murine BRCA1 deficient cells, another defect conferring radiosensitivity, in comparison with a BRCA1 proficient cell line. We transiently depleted BRCA1 by siRNAs in two human mammary epithelial cell lines but could not find changes in telomere length in comparison with control cells. Cytological evidence of telomere dysfunction was observed in all radiosensitive cell lines. These results suggest that mechanisms that confer sensitivity to IR may be linked with mechanisms that cause telomere dysfunction. Furthermore, we have been able to show that human ALT positive cell lines show dysfunctional telomeres as detected by either the presence of DSBs at their telomeres or cytogenetic analysis and usually cells with dysfunctional telomeres are sensitive to IR. Finally, we assessed hTERT mRNA splicing variants and telomerase activity in brain tumours, which exhibit considerable chromosome instability suggesting that DNA repair mechanisms may be impaired. We demonstrated that high levels of hTERT mRNAs and telomerase activity correlate with proliferation rate. The presence of hTERT splice variants did not strictly correlate with absence of telomerase activity but hTERT spliced transcripts were observed in some telomerase negative brain tumours suggesting that hTERT splicing may contribute to activation of ALT mechanisms.

All organisms respond to breaks in the DNA by promptly launching the DNA-damage response (DDR). This involves the recruitment of DNA repair proteins to sites of DNA damage and the activation of “checkpoint” activities that slow down or arrest cell-cycle progression, thus delaying key cell cycle transitions until the damage has been removed. In multicellular organisms, the inability to repair DNA damage and/or prolonged checkpoint activation can lead to programmed cell death or cause the cell to enter a permanent cell cycle arrest known as cellular senescence. The goal of my PhD period was to understand the mechanisms that lead to cellular senescence as opposite to transient checkpoint activation and to discover the role of novel modulators of the senescence condition, always in relation to DDR functions. It has been previously shown that telomere-initiated cellular senescence is associated with the activation of DDR. In my PhD thesis, I have shown that a DDR is persistently active during cellular senescence and it is necessary for its maintenance. I also investigated how the DDR signalling pathway remains active up to years after initial senescence establishment. My results support the conclusion that the presence of persistent DDR foci in senescent cells is due to their intrinsic irreparability. I therefore believe that the difference between transient checkpoint activation and senescence is the presence, in the latter, of irreparable DNA damage leading to protracted DDR signalling. I next attempted to probe the molecular features of irreparable DNA breaks. I discovered that exposing human normal fibroblasts to ionizing radiation can lead to the generation of DNA damage, a small portion of which, is not repairable. Therefore not all DNA breaks are efficiently repaired in the human genome. I also observed that persistent DDR is preferentially located at the telomeres or in their proximities. My present working hypothesis is that if DNA damage occurs at a telomeric site, it is not efficiently repaired and this leads to a chronic DDR activation. I also extended these observations to DNA damaging agents commonly used in cancer therapy and known to induce cellular senescence. I observed that also these compounds lead to the preferential generation of irreparable DNA damage in close proximity to telomeric tracts. Thus, my data indicate that telomeres are sinks of irreparable DNA damage and that are a genomic locus that, once damaged, enforces senescence. In this thesis, I also discuss my contribution to another project being pursued in my group, namely the study of the mechanisms that cause DDR activation in oncogene-induced senescence (OIS). In particular, I studied the contribution of reactive oxygen species (ROS) production following oncogenic Ras expression. I found that ROS are mitogenic mediators of oncogenic Ras and play a causative role in OIS by sustaining the hyperproliferation phase preceding OIS establishment. My results therefore highlight an unanticipated role of ROS in mediating senescence. In addition to their cell-autonomous functions, senescent cells can alter the tissue microenvironment and affect neighbouring cells through paracrine signalling. This phenomenon is mediated by the secretion of various chemokines and chemokine receptors. In this thesis, I describe the results obtained in a collaborative project with the Cell Proliferation Group (MRC Clinical Sciences Centre, Imperial College, London, UK) lead by Jesus Gil, in which I studied the contribution of the chemokine receptor CXCR2 in OIS. I discovered that CXCR2 control DDR functions both in transient checkpoint assays and in senescent cells. My results therefore indicate that DDR is controlled also by extracellular cues. Finally, in the appendix of my PhD thesis, I will present some results that I obtained during the first two years of my PhD program, but despite further investment in terms of time and efforts, we decided not to purse any further. These data point to a potential link between ROS, senescence and DDR activation. Indeed, it is already known that cellular senescence and aging are associated with an increase of cellular oxidative stress. In my study, I highlighted a signalling active role of ROS in maintenance of cellular senescence, in the absence of activated oncogenes: I found that the mitochondrial ROS increase observed both in telomere dysfunctional-induced and in irradiation-induced cellular senescence, and ROS play a role in mediating the signalling cascade that sustains DDR activation, therefore positively controlling the maintenance of the senescence state.

Les extrémités des chromosomes comportent le télomère puis la région sous télomérique. Ces deux domaines se distinguent des autres régions chromosomiques car ils évoluent par des échanges entre les chromosomes hétérologues. Le télomère est une structure spécialisée constituant la fin des chromosomes et indispensable à leur stabilité. Il joue un rôle important dans l'organisation spatiale des chromosomes en particulier dans l'agglutination des extrémités chromosomiques en périphérie nucléaire. La région sous télomérique, adjacente au télomère est très redondante entre les chromosomes hétérologues et se termine avec les séquences uniques spécifiques à chaque chromosome. Sa fonction ainsi que sa structure ne sont pas bien connues. Plusieurs familles de séquences répétées y sont présentes. Certaines sont localisées uniquement à proximité du télomère, d'autres comme les minisatellites sont en majorité localisées dans les derniers mégabases des chromosomes. Nous avons étudié en détail une région sous télomérique présente sur une dizaine de chromosomes chez tous les individus. Nous montrons qu'elle s'est propagée par des translocations successives de domaines chromosomiques terminaux de 80 a 200 Kb, impliquant des processus de recombinaison divers. Ces translocations se sont produites après la séparation de l'homme et du chimpanzé. La stabilité de la région apparaît variable suivant les chromosomes ce qui se traduit par un polymorphisme des localisations de la région entre les individus. Cette région sous télomérique a évolué de façon très différente entre l'homme et le chimpanzé. Nous proposons que cette évolution pourrait être conditionnée par la présence de gènes adjacents à la région sous télomerique. Nous avons en effet montré que des gènes ubiquitaires se trouvent à quelques dizaines de Kb en aval de la région sous télomérique. Leur expression pourrait être influencée par la chromatine adjacente, c'est à dire par la nature de la région sous télomérique. Nous proposons enfin que l'évolution de la région sous télomérique constitue un modèle pour l'étude de l'évolution du génome humain.

Preimplantation genetic diagnosis (PGD) refers to the testing of embryos produced through in vitro fertilization (IVF) in order to identify those unaffected by a specific genetic disorder or chromosomal abnormality. In this study, different methodologies were examined and developed for performance of PGD. Investigation of various whole genome amplification (WGA) methods identified multiple displacement amplification as a reliable method for genotyping single cells. Furthermore, this technology was shown to be compatible with subsequent analysis using single nucleotide polymorphism (SNP) microarrays. Compared to conventional methods used in this study to perform single cell diagnosis (e.g. multiplex PCR), WGA techniques were found to be advantageous since they streamline the development of PGD protocols for couples at high risk of transmitting an inherited disorder and simultaneously offer the possibility of comprehensive chromosome screening (CCS). This study also aimed to develop a widely applicable protocol for accurate typing of the human leukocyte antigen (HLA) region with the purpose of identifying embryos that will be HLA-identical to an existing sibling affected by a disorder that requires haematopoietic stem cell transplantation. Additionally, a novel microarray platform was developed that, apart from accurate CCS, was capable of reliably determining the relative quantity of mitochondrial DNA in polar bodies removed from oocytes and single cells biopsied from embryos. Mitochondria are known to play an important role in oogenesis and preimplantation embryogenesis and their measurement may therefore be of clinical relevance. Moreover, real-time PCR was used for development of protocols for CCS, DNA fingerprinting of sperm samples and embryos and the relative quantitation of telomere length in embryos (since shortened telomeres might be associated with reduced viability). As well as considering the role of genetics in terms of oocyte and embryo viability assessment and the diagnosis of inherited genetic disorders, attention was given to a specific gene (Phospholipase C zeta) of relevance to male infertility. A novel mutation affecting the function of the resulting protein was discovered highlighting the growing importance of DNA sequence variants in the diagnosis and treatment of infertility.

Le maintien de l'intégrité du génome est essentiel pour la survie cellulaire et la propagation de l'information génétique. Une mauvaise prise en charge des dommages de l’ADN et / ou une aberration de la maintenance de l’intégrité des télomères - les extrémités des chromosomes linéaires - provoquent chez l'homme des pathologies associées à une instabilité génétique. Ainsi, des dysfonctions télomériques sont à l’origine de la Dyskératose Congénitale (DC), et de sa forme rare et sévère, le Syndrome de Hoyeraal-Hreidarsson (HHS). Les DC et HHS se caractérisent principalement par une insuffisance médullaire progressive, des défauts développementaux et une prédisposition à développer des cancers. Par ailleurs, de nombreux syndromes associant déficits immunitaires et anomalies développementales sont causés par des défauts de réparation de l'ADN (cas de déficits immunitaires sévères, de l’Anémie de Fanconi (FA), de l’ataxie télangiectasie (AT), etc …). Au cours de ce travail, nous avons réalisé une étude phénotypique et génétique de patients atteints de deux pathologies aux caractéristiques cliniques distinctes. Ce travail de thèse a permis : 1) d'une part d'identifier des mutations de RTEL1 chez 3 patients atteints de HHS, décrivant ainsi une nouvelle cause moléculaire de cette pathologie. L'analyse des cellules de ces patients a révélé le rôle crucial que joue RTEL1 sur la stabilité du génome et le maintien des télomères dans des cellules humaines. 2) d'autre part, d'identifier un défaut en MYSM1, une histone déubiquitinase, dans un nouveau syndrome immuno-hématologique associé à des défauts de réparation de l’ADN présentant certaines similitudes avec l'anémie de Fanconi. Cette étude démontre pour la première fois, qu'outre son rôle dans la régulation transcriptionnelle, MYSM1 participe également aux mécanismes de réparation des lésions de l'ADN
Maintaining genome integrity is essential for cell survival and propagation of the genetic information. Improper management of DNA damages and / or aberrations in maintenance of telomere - the ends of linear chromosomes - causes humans disorders associated with genetic instability. Thus, in humans, telomere dysfunction causes Dyskeratosis Congenita (DC), and its rare and severe form, Hoyeraal-Hreidarsson Syndrome (HHS). DC and HHS are mainly characterized by progressive bone marrow failure, developmental defects and predisposition to cancer. In addition, many syndromes involving immunodeficiency and developmental abnormalities are caused by defects in DNA repair (e.g. severe immune deficiencies, Fanconi Anemia (FA), Ataxia Telangiectasia (AT),…). In this work, we performed a phenotypic and genetic study of patients with two syndromes presenting distinct clinical features. This work permitted : 1) on one hand, to identify RTEL1 mutations in patients with HHS and describe a new molecular cause of this disease. The analysis of patients’ cells revealed the crucial role for RTEL1 in genome stability and telomere maintenance in human cells. 2) on the other hand, to identify mutations in MYSM1, a histone deubiquitinase, in a new immuno-hematological syndrome associated with defects in DNA repair and sharing some similarities with Fanconi anemia. This study demonstrates for the first time that, in addition to its role in transcriptional regulation, MYSM1 is required to cope with DNA damages

Les lymphocytes constituent un modèle original de cellules somatiques puisqu’ils sont capables de réactiver la télomérase lorsqu’ils sont stimulés. Nous avons montré que les lymphocytes, en culture prolongée et soumis à des stimulations itératives par la PHA, présentent une diminution progressive de l’activité télomérasique interrompue à chaque stimulation par une augmentation transitoire. Ces variations sont corrélées positivement aux variations de hTERT et de la longueur des télomères. Les foyers γ-H2AX et 53BP1 et leur localisation au niveau des télomères augmentent lors du vieillissement cellulaire. Nous montrons un dysfonctionnement des télomères au cours de la sénescence lymphocytaire in vitro résultant d’une érosion accrue des télomères et d’une diminution de l’expression des protéines qui les coiffent. Le mécanisme des variations précoces de l’expression de hTERT lors de l’activation lymphocytaire restaient à comprendre. Les conséquences du traitement des lymphocytes par différents immunosuppresseurs agissant tous de façon directe ou indirecte sur l’activation de NFAT suggéraient le rôle de NFAT dans la régulation transcriptionnelle de hTERT. Nous avons montré i) 5 éléments de réponse potentiels pour NFAT au niveau du promoteur de hTERT, ii) l’activation in vitro du promoteur de hTERT par NFAT essentiellement via un site consensus localisé dans le coeur du promoteur de hTERT en position -40 et une synergie fonctionnelle entre NFAT et SP1, iii) la liaison directe de NFAT sur le promoteur de hTERT via ce site consensus in vivo. Ainsi, NFAT1 régule la transcription de hTERT et est impliqué dans l’activation de la télomérase lors de la stimulation lymphocytaire
Lymphocytes are an example of somatic cells capable to induce telomerase activity when stimulated. We showed that lymphocytes, during long-term culture and repeated PHA stimulations, present a progressive drop in telomerase activity interrupted at each stimulation by a transitory increase. These variations are positively correlated with hTERT and telomere length variations. γ-H2AX and 53BP1 foci and their localization on telomeres increase with cell aging. We show a telomere dysfunction during in vitro lymphocyte senescence resulting from an excessive telomere shortening and a decrease in shelterin content. The mechanism involved in early variations of hTERT expression during lymphocyte activation remained to be understood. Consequences of lymphocyte treatment with different immunosuppressors, all acting directly or indirectly on NFAT activation, suggested a role for NFAT in the regulation of hTERT transcription. Five putative responsive elements for NFAT were identified in the hTERT promoter. We showed that NFAT activates in vitro the hTERT promoter mainly via a consensus site localized in the promoter core at position -40 and a functional synergy between NFAT and SP1. Furthermore, NFAT1 binds directly to the endogenous hTERT promoter via this consensus site in vivo. Thus, NFAT positively regulates the hTERT transcription and we propose its implication in telomerase activation during lymphocyte stimulation

博士
國立臺灣師範大學
化學系
99
Telomeres, the ends of eukaryotic chromosomes, are essential for the stability of chromosomes. In the presence of monovalent cations such as Na+ or K+, the G-rich single stranded DNA of telomere can form a secondary structure through Hoogsteen hydrogen bonds, termed G-quadruplex (G4). We have applied two-photon excitation fluorescence lifetime microscope (2PE-FLIM) to successfully verify and map the localizations of G4 structures in human nasopharyngeal carcinoma metaphase chromosomes. In addition, the G-rich sequences can adopt various G4 structures and possibly interconvert among these structures upon changing solvent and temperature conditions. For example, a fast spectral conversion occurs under Na/K cation exchange. We have developed a number of methods to elucidate the mechanisms of this spectral conversion. Ensemble-based fluorescence resonance energy transfer (FRET) and single molecule tethered particle motion (TPM) studies suggested that the fast spectral conversion is unlikely due to F1UFF2 via a totally unfolded intermediate induced by potassium cations. In addition, temperature-dependent circular dichroism (CD) studies suggested that the energy barrier from F1 to F2 is almost negligible. Thus, we consider that the fast spectral conversion during Na/K cation exchange is due to F1F2 via rapid base shift and loop rearrangement. On the other hand, the structural conversion from the antiparallel G4 structure in Na+ solution to the parallel G4 structure in K+ solution was observed in the presence of dehydrated reagents. Using thermodynamic and kinetic studies, a free energy diagram can be tentatively established for the structural conversion of HT22 from antiparallel form in Na+ solution to the parallel in K+ solution at 25℃ under 40 % (w/v) PEG 200 condition. It is known that the Cu2+ induces the unfolding of G4 structure while addition of the EDTA2- can chelate the Cu2+ to reverse the unfolded state to the folded state. Based on this and we found that the kinetic product is likely to play a major role in physiological condition. Furthermore, G4 stabilizers are screened by a novel method based on Cu2+ -induced G4 unfolding at room temperature. Thus, 3,6,9 tri-substitution of BMVC4 core molecules are ready to prepare in further study.

碩士
國立陽明大學
生物醫學資訊研究所
105
In mitosis, the chromosomes of the cell are shortened with the number of processes. The human telomere is a repeat of the “TTAGGG” sequence at the end of the chromosome and its function plays a key role during cell replication processes such as recombination and degradation. In stem cells and cancer cells, a telomere-preserving enzyme, telomerase is activated to maintain the length of telomere. When the telomere forms a specific tertiary structure, G-quadruplex, it can’t be recognized and repaired by telomerase. Therefore, G-quadruplex is a crucial target for anticancer drug development. The topology of the G-quadruplex structure depends on its anti/syn pattern, the types of connecting loops, the nature of bound cations, the number of quartets, the strand orientation, and the presence or absence of additional nucleotides at the tails of the strands. Understanding the mechanism of conformational changes of G-quadruplex is important in drug designs. Because it is difficult to generate unfavorable states using the conventional molecular dynamics (MD) simulation, we herein perform targeted molecular dynamics (TMD) and umbrella sampling methods to investigate these problems. The TMD is to apply a guiding potential along a reaction coordinate to generate the initial coordinate for the umbrella sampling computations. Upon the umbrella sampling along the reaction coordinate, the potential of mean force (PMF) can be calculated. Because there are multiple pathways of conformational transitions of the G-quadruplex, a principal component analysis is used to reduce the multiple reaction coordinates to two-dimensional (2D) reaction coordinates. A 2D energy contour map is constructed. The zero-temperature string method (ZTS) is used to find the most possible pathway in the reaction coordinate. Our results show that the stability of G-quadruplex structures can be enhanced and the path of the conformation transition would be changed in the presence of cations.

碩士
國立臺灣大學
化學研究所
102
We used an optical tweezers platform to study the folding and unfolding pathway of individual molecules containing single-stranded DNA human telomeric G-quadruplex (G4) sequence, (TTAGGG)4. We home-built an optical tweezers platform with force-clamp capability, which held a DNA tether at a constant force, to determine the DNA length in high spatro-temperal resolution. We included an acousto-optic modulator (AOM) to maintain the laser stability and madulate laser output intensity. By modulating the applied voltage of AOM, feedbacked from the laser power measurement, we achieved to maintain the laser power with standard deviation less than 0.01mW over 20 minutes. For G4 experiments, these G4 containing DNA molecules are found to form the G-quadruplex structure based on Hoogsteen basepairing in 150 mM Na+ solution. When forces were applied to unfold the G4-containing DNA molecules, most of the unfolding traces showed one or two transitions, suggesting the existence of one stable intermediate state. The total unfolding distance was consistent with the expected value of unfolded G4 structure. However, when the DNA molecules were pre-incubated with a G4 stabilizing ligand BMVC, 3,6-bis(1-methyl-4-vinylpyridinium) carbazole, most DNA molecules showed three unfolding transitions, suggesting of two stable unfolding intermediate states. Using the force-clamp assay, we found that three extension states exist in the traces of G4 DNA. When G4 was pre-incubated with BMVC, the number of extension states also increases to four. Both force-extension and force-clamp results suggest that BMVC-bound G4 structures are able to withstand higher force than the ligand-free G4 structure, thus revealing more intermediate states.

Meiotic recombination is a prerequisite for exchange of genetic information in all Sexually reproducing organisms. This process is initiated by the formation of double stranded breaks (DSBs) in DNA followed by homology directed repair. The process is subjected to surveillance mechanisms that control DSB formation and allow for repair of DSBs by halting cell cycle progression. Interestingly, though generation of DSBs is an Essential event in meiosis they are nevertheless regarded as the most lethal forms of DNA damage. If left unrepaired a single DSB can lead to gene deletion, duplication, translocations and missegregation of large chromosome fragments leading to cell death. In Saccharomyces cerevisiae, genetic screens for mutants defective in meiotic recombination led to the identification of a group of genes called the RAD52 epistasis group which includes RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, RAD59, MRE11 and XRS2. A subset of these genes, namely MRE11, RAD50 and XRS2, have been shown by genetic studies to be essential for several nuclear events including sensing DSBs, double strand break repair (DSBR) by homologous recombination (HR) and non homologous end joining (NHEJ), telomere length maintenance, cell cycle activation in response to DSBs, mitotic and meiotic recombination. In vitro, Mre11 displays Mn2+-dependent endonuclease activity on ssDNA, 3'-5' Exonuclease on single- and double-stranded DNA, strand annealing and weak hairpin Opening activities. Mutational analyses have revealed two functional domains in Mre11- Then terminal nuclease domain involved in telomere length maintenance and DSB Processing and the C terminal DNA binding domain involved in DSB formation during Meiosis. Rad50, a 153 kDa protein shares homology with the SMC (Structural Maintenance of Chromosome) family of proteins which are involved in chromosome Condensation and cohesion. It consists of a bipartite N- and C terminal Walker A and Walker B motifs separated by a heptad repeat sequence which folds into an antiparallel Coiled-coil structure. The heptad repeats are separated by a metal binding globular region the Zn hook. Rad50 is an ATP-dependent DNA-binding protein. hRad50 regulates the exonuclease activity of hMre11. Unlike Mre11 and Rad50, which are evolutionarily conserved, Xrs2 is found only in S. cerevisiae and Nbs1 in mammals. Xrs2 appears to be sequence non-specific DNA- binding protein. Xrs2 in yeast or Nbs1 is its counterpart in mammals target Mre11 and Rad50 to the sites of DNA damage and mediate S-phase cell cycle checkpoint activation. Mutations in either one of the MRX subunits results in defects in repair of DSBs, activation of cell cycle checkpoint and shortened telomeres leading to genomic instability. Hypomorphic mutations in MRE11 and NBS1 lead to genetic disorders- A-TLD (ataxia-telangiectasia-like disorder) and NBS (Nijmegen breakage syndrome) respectively, that are phenotypic ally related to AT (ataxia-telangiectasia) caused by mutations in ATM. Patients with AT, A-TLD or NBS syndromes are hypersensitive to radiomimetic agents and are predisposed to cancer. Several lines of evidence suggest that S. cerevisiae strains bearing mre11Δ, rad50Δ or xrs2Δ display shortening of telomeres. Telomeres are the nucleoprotein ends of all linear eukaryotic chromosomes that are important in maintaining the integrity of the genome.Telomeres are comprised of repetitive G rich sequence most of which is double stranded but the extreme 3' end protrudes to form 3' single stranded overhang called the G tail. elopers are essential in preventing end-end fusion of chromosome, are important for chromosome replication, segregation and genome stability. Genetic studies have implicated the MRX complex in both telomerase-dependent and independent telomere length maintenance. Studies have indicated a direct role for S. cerevisiae MRE11 in the proper establishment of telomere end-structure. However, the molecular mechanism of MRX at telomeres is poorly understood. To understand the role(s) of MRX complex at telomeres, it is important to elucidate the biochemical activities of MRX complex as well as its individual subunits on the telomere DNA structures. Since, Mre11 complex is known to function in several processes related to DNA metabolism it becomes imperative to study the function of Mre11 complex on DNA substrates in the context of a given nuclear process. The 3' single trended telomeric sequence is capable of acquiring folded conformation(s) as a mechanism of end protection which is mediated by several telomere-specific and nonspecific ending proteins. In mammals, the 3' ssDNA has been demonstrated to fold into tloop configuration mediated by some of the components of sheltrin protein complex, wherein the ssDNA invades the duplex DNA resulting in the formation of a displacement loop (D loop). Evidence for the formation of t-loop has been shown in vitro with human telomeres. However, the formation of t-loops has not been demonstrated in S. cerevisiae. Nevertheless, there is growing body of evidence which suggests the formation of alternative DNA structures such as G4 DNA at the yeast telomeres. G quadruplexes (G quartets or G4 DNA) are thermodynamically stable structures formed by Hoogsteen base pairing between guanine residues. In a G quartet the four guanine residues are paired, where each guanine residue is an electron acceptor and a donor and stabilized by a metal cation. The presence of G rich motifs at the promoter regions, rDNA, telomeres and recombination hot spots indicate that G4 DNA has important functions in vivo. Although the existence of G4 DNA has been the subject of much debate, the identification of several proteins that promote (Rap1, Hop1, Topo I, TEBPβ), modify and resolve (POT1, TERT, KEM1, GQN1, BLM, WRN, Rte1) G4 DNA, together with the direct visualization of G4 DNA using G4 DNA specific antibodies and RNA interference have provided compelling for the existence of G4 DNA in vivo. To elucidate the function of MRX complex or its individual subunits at telomeres, the biochemical activities of purified MRX complex and its individual subunits on G4 DNA, D loop, duplex DNA and G rich ssDNA has been analyzed in this study. G4 DNA was assembled from S. cerevisiae telomeric sequence. G4 DNA was isolated and its identity was ascertained by chemical probing and circular dichroism. S. cerevisiae MRE11 and XRS2 was cloned and expressed in E. coli BL21 (DE3)plysS. S. cerevisiae RAD50 in pPM231 vector in S. cerevisiae BJ5464 strain was a gift from Dr. Patrick Sung (Yale University). Mre11, Rad50 and Xrs2 were overexpressed and purified to >98% homogeneity. The identity of the proteins was ascertained by Western bloting using polyclonal antibodies. Using purified proteins heterotrimeric MRX and heterodimeric MR and MX protein complexes were formed in the absence of ATP, DNA or Mn2+. The ability of M/R/X to bind to telomeric DNA substrates was studied by electrophoretic mobility shift assays. Mre11, Rad50, Xrs2 and MRX displayed higher binding affinity for G4 DNA over D loop, ss- or dsDNA. MRX bound G4 DNA more efficiently compared to its individual subunits as 10-fold lower concentration of MRX was able to shift the DNA into the protein-DNA complex. The protein-G4 DNA complexes were stable as >0.8 M NaCl as required to dissociate 50% of protein-G4 DNA complexes. Efficient competition by poly(dG), which is known to fold into G4 DNA, suggested that the protein-G4 DNA complex was specific. Competition experiments with tetra-[N-methyl- pyridyl]-porphyrin suggested that M/R/X recognizes distinct determinants and makes specific interactions with G4 DNA. G4 DNA is highly polymorphic and can exist as intramolecular or intermolecular (parallel and antiparallel) structures. High affinity binding of Mre11 to G4 DNA (parallel) over G2' DNA (antiparallel), ss- and dsDNA suggests the existence of parallel G4 DNA structures at the telomeres and that G4 DNA may be the natural substrate for MRX complex in vivo. Telomeres are elongated by telomerase that requires access to the 3' G-tail for its activity. Formation of G4 DNA structures renders the 3' G-tail inaccessible to telomerase thereby inhibiting telomere elongation. To elucidate the functional relevance of high affinity of M/R/X for G4 DNA, the ability of the complex to generate the appropriate DNA structure for telomere elongation has been analyzed. In this study, I considered the possibility that MRX could act as: (a) a helicase that opens up the G4 DNA structures making it accessible to telomerase or (b) as a nuclease that cleaves the G4 DNA generating substrates for telomerase. Helicase assay with Mre11, Xrs2, MX and MRX on G4 DNA and duplex DNA showed no detectable DNA unwinding activity. Interestingly, nuclease assays with Mre11 on G4 DNA showed that Mre11 cleaved G4 DNA in Mn2+-dependent manner and the cleavage was mapped to the G residues at the stacks of G quartets. Mre11 cleaved telomeric duplex DNA in the center of TGTG repeat sequence, G rich ssDNA at 5' G residue in an array of 3 G residues and D loop structure preferentially at the 5' ends at TG residues. Significantly, the endonuclease activity of Mre11 was abrogated by Rad50. Xrs2 had no effect on the endonuclease activity of Mre11. Structural studies on Rad50 and Mre11 showed that binding of ATP by Rad50 positions the Rad50 catalytic domain in close proximity to the nuclease active site of Mre11. In yeast, disruption of ATP binding Walker motifs results in a null phenotype, suggesting that ATP is required for Rad50 functions in vivo. hRad50 is known to regulate the exonuclease activity of hMre11 in the presence of ATP. Therefore, can ATP modulate the effect of S. cerevisiae (Sc) Rad50 on ScMre11? To address this question, I monitored the ATPase activity of Rad50 in the absence or presence of DNA. Rad50 hydrolyzed ATP in a DNA-independent manner; however, ATPase activity was enhanced in the presence of Mre11 and Xrs2. However, Rad50 exhibited a low turnover indicating that ATP could function as a switch molecule. Based on these observations, the effect of ATP on the nuclease activity was examined. The binding of ATP and its hydrolysis by Rad50 attenuated the inhibition exerted by Rad50 on the Mre11 endonuclease activity. Cleavage of G4 DNA, D loop, duplex DNA and ssDNA required ATP hydrolysis, since no cleavage product was observed when ADP or ATPγS was substituted for ATP. This observation was corroborated using a hairpin DNA substrate that mimics a intermediate in VDJ recombination, thereby confirming the generality of regulation of Rad50 on the endonuclease activity of Mre11. Does Rad50 regulate the exonuclease activity of Mre11 as well? To address this question, exonuclease activity of Mre11, MR and MRX on 3' labeled duplex DNA and G4 DNA was assayed. Rad50 had no measurable effect on the exonuclease activity of Mre11. Based on previous studies and my observations, I propose a model for the role of MRX in telomere length maintenance and its regulation by the ATP-binding pocket of Rad50. MRX binds telomeric DNA substrates in a non-productive complex, which is converted to a catalytically active complex upon binding of ATP by Rad50. ATP induces conformational changes, repositioning the complex such that the catalytic site of Mre11 now has access to the substrate. Following cleavage of DNA by Mre11, the release of ADP and inorganic phosphate, generate the cleaved product. The cleaved DNA is now accessible to telomerase or telomere binding proteins. In summary, the data presented in my PhD thesis demonstrates that Mre11 is a structure- and sequence-specific endonuclease. The natural substrate for telomerase is the 3' ssDNA. G quartets at telomeres not only protect the ends from degradation but also make the ends inaccessible for telomerase activity. Genetic studies have shown that cells proficient for telomerase activity but lacking any one of the components of the MRX complex display shortening in telomere length. The ability of Mre11 to cleave G4 DNA at the stacks of G quartets therefore, suggests a mechanism by which the 3' ssDNA is rendered accessible to telomerase or other telomere binding proteins. Yeast telomeres are characterized by the presence of subtelomeric Y' elements proximal to the terminal TG1- 3 repeat sequences. The Y' element has been shown to be amplified by telomerase in a fraction of mutants with short telomeres. The mechanism by which Y' DNA is amplified is unclear. The ability of Mre11 to cleave telomere duplex DNA at the center of TGTG repeats could contribute to the generation of appropriate substrate for elongation by telomerase, thereby contributing to Y' DNA amplification. Telomere length is maintained by homeostasis between processes that contribute to telomere elongation and those that cause attrition in telomeric ends. Overelongated telomeres are brought to wild type telomere size by a unique recombinational single step deletion process termed telomere rapid deletion (TRD). TRD involves invasion of the elongated 3' G tail into the proximal telomeric tract resulting in the formation of the D loop structure. Following branch migration the D-loop is nicked and resolved into a deleted telomere and a circular liner product. Cells deleted for MRE11, RAD50 or XRS2 are deficient in TRD process. It has been hypothesized that Mre11 could be a candidate for cleaving the D-loop structure. The endonuclease activity of Mre11 on D-loop structure, preferentially at the 5' ends at TG residues demonstrated in this study, show that Mre11 could function as the nuclease required to generate the deleted telomere in TRD. MRX complex is involved in several processes involving DNA metabolism. It is important that the activities of the complex are regulated in the in vivo context. Complex formation and the interaction of the individual subunits with nucleotide cofactors and metal ions constitute a mode of regulation. This study shows that Rad50 regulates the endonuclease, but not exonuclease activity of Mre11. The binding of ATP and its hydrolysis by Rad50 brings in the regulatory factor necessary to keep the uncontrolled nuclease activity of MRX in check, thus preventing any deleterious effects on telomere length. Telomere maintenance by telomerase is activated in 80% of cancer cells. Inhibition of telomerase by G quartets provides a new drug targets for potential anti-cancer drugs. It is, therefore, likely that understanding the biological consequences of G quadruplex interactions would provide a better insight in development of therapeutics for cancer.

Meiotic recombination is a prerequisite for exchange of genetic information in all Sexually reproducing organisms. This process is initiated by the formation of double stranded breaks (DSBs) in DNA followed by homology directed repair. The process is subjected to surveillance mechanisms that control DSB formation and allow for repair of DSBs by halting cell cycle progression. Interestingly, though generation of DSBs is an Essential event in meiosis they are nevertheless regarded as the most lethal forms of DNA damage. If left unrepaired a single DSB can lead to gene deletion, duplication, translocations and missegregation of large chromosome fragments leading to cell death. In Saccharomyces cerevisiae, genetic screens for mutants defective in meiotic recombination led to the identification of a group of genes called the RAD52 epistasis group which includes RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, RAD59, MRE11 and XRS2. A subset of these genes, namely MRE11, RAD50 and XRS2, have been shown by genetic studies to be essential for several nuclear events including sensing DSBs, double strand break repair (DSBR) by homologous recombination (HR) and non homologous end joining (NHEJ), telomere length maintenance, cell cycle activation in response to DSBs, mitotic and meiotic recombination. In vitro, Mre11 displays Mn2+-dependent endonuclease activity on ssDNA, 3'-5' Exonuclease on single- and double-stranded DNA, strand annealing and weak hairpin Opening activities. Mutational analyses have revealed two functional domains in Mre11- Then terminal nuclease domain involved in telomere length maintenance and DSB Processing and the C terminal DNA binding domain involved in DSB formation during Meiosis. Rad50, a 153 kDa protein shares homology with the SMC (Structural Maintenance of Chromosome) family of proteins which are involved in chromosome Condensation and cohesion. It consists of a bipartite N- and C terminal Walker A and Walker B motifs separated by a heptad repeat sequence which folds into an antiparallel Coiled-coil structure. The heptad repeats are separated by a metal binding globular region the Zn hook. Rad50 is an ATP-dependent DNA-binding protein. hRad50 regulates the exonuclease activity of hMre11. Unlike Mre11 and Rad50, which are evolutionarily conserved, Xrs2 is found only in S. cerevisiae and Nbs1 in mammals. Xrs2 appears to be sequence non-specific DNA- binding protein. Xrs2 in yeast or Nbs1 is its counterpart in mammals target Mre11 and Rad50 to the sites of DNA damage and mediate S-phase cell cycle checkpoint activation. Mutations in either one of the MRX subunits results in defects in repair of DSBs, activation of cell cycle checkpoint and shortened telomeres leading to genomic instability. Hypomorphic mutations in MRE11 and NBS1 lead to genetic disorders- A-TLD (ataxia-telangiectasia-like disorder) and NBS (Nijmegen breakage syndrome) respectively, that are phenotypic ally related to AT (ataxia-telangiectasia) caused by mutations in ATM. Patients with AT, A-TLD or NBS syndromes are hypersensitive to radiomimetic agents and are predisposed to cancer. Several lines of evidence suggest that S. cerevisiae strains bearing mre11Δ, rad50Δ or xrs2Δ display shortening of telomeres. Telomeres are the nucleoprotein ends of all linear eukaryotic chromosomes that are important in maintaining the integrity of the genome.Telomeres are comprised of repetitive G rich sequence most of which is double stranded but the extreme 3' end protrudes to form 3' single stranded overhang called the G tail. elopers are essential in preventing end-end fusion of chromosome, are important for chromosome replication, segregation and genome stability. Genetic studies have implicated the MRX complex in both telomerase-dependent and independent telomere length maintenance. Studies have indicated a direct role for S. cerevisiae MRE11 in the proper establishment of telomere end-structure. However, the molecular mechanism of MRX at telomeres is poorly understood. To understand the role(s) of MRX complex at telomeres, it is important to elucidate the biochemical activities of MRX complex as well as its individual subunits on the telomere DNA structures. Since, Mre11 complex is known to function in several processes related to DNA metabolism it becomes imperative to study the function of Mre11 complex on DNA substrates in the context of a given nuclear process. The 3' single trended telomeric sequence is capable of acquiring folded conformation(s) as a mechanism of end protection which is mediated by several telomere-specific and nonspecific ending proteins. In mammals, the 3' ssDNA has been demonstrated to fold into tloop configuration mediated by some of the components of sheltrin protein complex, wherein the ssDNA invades the duplex DNA resulting in the formation of a displacement loop (D loop). Evidence for the formation of t-loop has been shown in vitro with human telomeres. However, the formation of t-loops has not been demonstrated in S. cerevisiae. Nevertheless, there is growing body of evidence which suggests the formation of alternative DNA structures such as G4 DNA at the yeast telomeres. G quadruplexes (G quartets or G4 DNA) are thermodynamically stable structures formed by Hoogsteen base pairing between guanine residues. In a G quartet the four guanine residues are paired, where each guanine residue is an electron acceptor and a donor and stabilized by a metal cation. The presence of G rich motifs at the promoter regions, rDNA, telomeres and recombination hot spots indicate that G4 DNA has important functions in vivo. Although the existence of G4 DNA has been the subject of much debate, the identification of several proteins that promote (Rap1, Hop1, Topo I, TEBPβ), modify and resolve (POT1, TERT, KEM1, GQN1, BLM, WRN, Rte1) G4 DNA, together with the direct visualization of G4 DNA using G4 DNA specific antibodies and RNA interference have provided compelling for the existence of G4 DNA in vivo. To elucidate the function of MRX complex or its individual subunits at telomeres, the biochemical activities of purified MRX complex and its individual subunits on G4 DNA, D loop, duplex DNA and G rich ssDNA has been analyzed in this study. G4 DNA was assembled from S. cerevisiae telomeric sequence. G4 DNA was isolated and its identity was ascertained by chemical probing and circular dichroism. S. cerevisiae MRE11 and XRS2 was cloned and expressed in E. coli BL21 (DE3)plysS. S. cerevisiae RAD50 in pPM231 vector in S. cerevisiae BJ5464 strain was a gift from Dr. Patrick Sung (Yale University). Mre11, Rad50 and Xrs2 were overexpressed and purified to >98% homogeneity. The identity of the proteins was ascertained by Western bloting using polyclonal antibodies. Using purified proteins heterotrimeric MRX and heterodimeric MR and MX protein complexes were formed in the absence of ATP, DNA or Mn2+. The ability of M/R/X to bind to telomeric DNA substrates was studied by electrophoretic mobility shift assays. Mre11, Rad50, Xrs2 and MRX displayed higher binding affinity for G4 DNA over D loop, ss- or dsDNA. MRX bound G4 DNA more efficiently compared to its individual subunits as 10-fold lower concentration of MRX was able to shift the DNA into the protein-DNA complex. The protein-G4 DNA complexes were stable as >0.8 M NaCl as required to dissociate 50% of protein-G4 DNA complexes. Efficient competition by poly(dG), which is known to fold into G4 DNA, suggested that the protein-G4 DNA complex was specific. Competition experiments with tetra-[N-methyl- pyridyl]-porphyrin suggested that M/R/X recognizes distinct determinants and makes specific interactions with G4 DNA. G4 DNA is highly polymorphic and can exist as intramolecular or intermolecular (parallel and antiparallel) structures. High affinity binding of Mre11 to G4 DNA (parallel) over G2' DNA (antiparallel), ss- and dsDNA suggests the existence of parallel G4 DNA structures at the telomeres and that G4 DNA may be the natural substrate for MRX complex in vivo. Telomeres are elongated by telomerase that requires access to the 3' G-tail for its activity. Formation of G4 DNA structures renders the 3' G-tail inaccessible to telomerase thereby inhibiting telomere elongation. To elucidate the functional relevance of high affinity of M/R/X for G4 DNA, the ability of the complex to generate the appropriate DNA structure for telomere elongation has been analyzed. In this study, I considered the possibility that MRX could act as: (a) a helicase that opens up the G4 DNA structures making it accessible to telomerase or (b) as a nuclease that cleaves the G4 DNA generating substrates for telomerase. Helicase assay with Mre11, Xrs2, MX and MRX on G4 DNA and duplex DNA showed no detectable DNA unwinding activity. Interestingly, nuclease assays with Mre11 on G4 DNA showed that Mre11 cleaved G4 DNA in Mn2+-dependent manner and the cleavage was mapped to the G residues at the stacks of G quartets. Mre11 cleaved telomeric duplex DNA in the center of TGTG repeat sequence, G rich ssDNA at 5' G residue in an array of 3 G residues and D loop structure preferentially at the 5' ends at TG residues. Significantly, the endonuclease activity of Mre11 was abrogated by Rad50. Xrs2 had no effect on the endonuclease activity of Mre11. Structural studies on Rad50 and Mre11 showed that binding of ATP by Rad50 positions the Rad50 catalytic domain in close proximity to the nuclease active site of Mre11. In yeast, disruption of ATP binding Walker motifs results in a null phenotype, suggesting that ATP is required for Rad50 functions in vivo. hRad50 is known to regulate the exonuclease activity of hMre11 in the presence of ATP. Therefore, can ATP modulate the effect of S. cerevisiae (Sc) Rad50 on ScMre11? To address this question, I monitored the ATPase activity of Rad50 in the absence or presence of DNA. Rad50 hydrolyzed ATP in a DNA-independent manner; however, ATPase activity was enhanced in the presence of Mre11 and Xrs2. However, Rad50 exhibited a low turnover indicating that ATP could function as a switch molecule. Based on these observations, the effect of ATP on the nuclease activity was examined. The binding of ATP and its hydrolysis by Rad50 attenuated the inhibition exerted by Rad50 on the Mre11 endonuclease activity. Cleavage of G4 DNA, D loop, duplex DNA and ssDNA required ATP hydrolysis, since no cleavage product was observed when ADP or ATPγS was substituted for ATP. This observation was corroborated using a hairpin DNA substrate that mimics a intermediate in VDJ recombination, thereby confirming the generality of regulation of Rad50 on the endonuclease activity of Mre11. Does Rad50 regulate the exonuclease activity of Mre11 as well? To address this question, exonuclease activity of Mre11, MR and MRX on 3' labeled duplex DNA and G4 DNA was assayed. Rad50 had no measurable effect on the exonuclease activity of Mre11. Based on previous studies and my observations, I propose a model for the role of MRX in telomere length maintenance and its regulation by the ATP-binding pocket of Rad50. MRX binds telomeric DNA substrates in a non-productive complex, which is converted to a catalytically active complex upon binding of ATP by Rad50. ATP induces conformational changes, repositioning the complex such that the catalytic site of Mre11 now has access to the substrate. Following cleavage of DNA by Mre11, the release of ADP and inorganic phosphate, generate the cleaved product. The cleaved DNA is now accessible to telomerase or telomere binding proteins. In summary, the data presented in my PhD thesis demonstrates that Mre11 is a structure- and sequence-specific endonuclease. The natural substrate for telomerase is the 3' ssDNA. G quartets at telomeres not only protect the ends from degradation but also make the ends inaccessible for telomerase activity. Genetic studies have shown that cells proficient for telomerase activity but lacking any one of the components of the MRX complex display shortening in telomere length. The ability of Mre11 to cleave G4 DNA at the stacks of G quartets therefore, suggests a mechanism by which the 3' ssDNA is rendered accessible to telomerase or other telomere binding proteins. Yeast telomeres are characterized by the presence of subtelomeric Y' elements proximal to the terminal TG1- 3 repeat sequences. The Y' element has been shown to be amplified by telomerase in a fraction of mutants with short telomeres. The mechanism by which Y' DNA is amplified is unclear. The ability of Mre11 to cleave telomere duplex DNA at the center of TGTG repeats could contribute to the generation of appropriate substrate for elongation by telomerase, thereby contributing to Y' DNA amplification. Telomere length is maintained by homeostasis between processes that contribute to telomere elongation and those that cause attrition in telomeric ends. Overelongated telomeres are brought to wild type telomere size by a unique recombinational single step deletion process termed telomere rapid deletion (TRD). TRD involves invasion of the elongated 3' G tail into the proximal telomeric tract resulting in the formation of the D loop structure. Following branch migration the D-loop is nicked and resolved into a deleted telomere and a circular liner product. Cells deleted for MRE11, RAD50 or XRS2 are deficient in TRD process. It has been hypothesized that Mre11 could be a candidate for cleaving the D-loop structure. The endonuclease activity of Mre11 on D-loop structure, preferentially at the 5' ends at TG residues demonstrated in this study, show that Mre11 could function as the nuclease required to generate the deleted telomere in TRD. MRX complex is involved in several processes involving DNA metabolism. It is important that the activities of the complex are regulated in the in vivo context. Complex formation and the interaction of the individual subunits with nucleotide cofactors and metal ions constitute a mode of regulation. This study shows that Rad50 regulates the endonuclease, but not exonuclease activity of Mre11. The binding of ATP and its hydrolysis by Rad50 brings in the regulatory factor necessary to keep the uncontrolled nuclease activity of MRX in check, thus preventing any deleterious effects on telomere length. Telomere maintenance by telomerase is activated in 80% of cancer cells. Inhibition of telomerase by G quartets provides a new drug targets for potential anti-cancer drugs. It is, therefore, likely that understanding the biological consequences of G quadruplex interactions would provide a better insight in development of therapeutics for cancer.

A number of studies have established that DNA targeting is a successful strategy in anticancer therapy. In recent years, however, the focus has shifted from double-stranded DNA to alternative DNA motifs such as G-quadruplex and i-motif structures that are often found in the telomeric and transcriptional regulatory regions of genes in almost all eukaryotic organisms. The mutually exclusive formation of G-quadruplex and i-motif structures by G/C rich sequences, which in turn impact a variety of DNA transactions, suggest that stabilization of such structures by small molecules offer alternative options for the treatment of genetic and life-style diseases. Indeed, a large number of G-quadruplex stabilizing ligands have been extensively studied for their anti-cancer activity both in vitro and in vivo. Acetyl-CoA carboxylase catalyses the ATP-dependent carboxylation of cytosolic acetyl-CoA to malonyl-CoA. The synthesis of malonyl-CoA is the first committed step for de novo fatty acid biosynthesis pathway. Numerous lines of evidence suggest that the expression and specific activity of acetyl-CoA carboxylase is highly regulated at transcriptional, translational, and post-translational levels. The expression of human acetyl-CoA carboxylase 1 gene (ACC1) is regulated by three alternative promoters (PI, PII, and PIII), but all three promoters produce the same protein coding sequence. Notably, promoter 1 and 2, but not promoter 3, harbour G/C-rich cis-elements whose secondary structure and function remain unknown. In the present study, using multiple complementary methods such as CD spectroscopy, FRET, electrophoretic mobility shift assay, chemical foot printing and computational methods we show that G-rich cis-elements of PI and PII promoters fold into thermodynamically stable G-quadruplex structures, and then establish unambiguously the topologies of these structures. Furthermore, we found that PI promoter folds into two distinct G-quadruplex structures with 1:1:1 loop arrangement, while PII promoter folds into 1:4:1 loop arrangement. Human nucleolin, a conserved major nuclear protein is known to regulate gene expression through interaction with G/C-rich sequences in the genome. We show that nucleolin binds to G-quadruplex DNA formed by ACC1 promoters with high specificity and in a dose-dependent manner. Most importantly, G-quadruplex formation in ACC1 gene promoter region blocks DNA replication, suppresses transcription, and this effect was further augmented by G-quadruplex stabilizing ligands. Taken together, these results not only demonstrate the existence of G-quadruplex structures in ACC1 promoters, but also attest to their functional significance. The formation of a G-quadruplex structure within a genomic duplex DNA region requires the separation of the G-rich strand from its complementary C-rich strand. As our study revealed that the G-rich sequences in ACC1 promoters, PI and PII, fold into G-quadruplex DNA, then the question arises whether the C-rich strand folds into i-motif structures. Using multiple complementary methods such as CD spectroscopy, FRET and electrophoretic mobility shift assay, we show that the C-rich sequences of PI and PII promoters fold into intramolecular imotif structures. The results of chemical foot printing assays indicated that whereas PI promoter folds into two distinct i-motif structures with 2:2:2 loop arrangements, PII promoter folds into 2:3:2 loop arrangement. Consistent with the significance of I-motif structures in the cellular context, we found that molecular crowding agents abet the formation of I-motif structures. These findings were ascertained by luciferase reporter activity assay. The data revealed that the C-rich sequence complementary to the G-rich sequence in ACC1 promoters markedly attenuated luciferase expression. The attenuated activity of the reporter could be unleashed by mutations in the C-rich sequence of ACC1 promoters. Several classes of small molecules that selectively stabilize G-quadruplex structures over duplex DNA are known. G-quadruplexes adopt a wide range of conformations and thus the ligands that can stabilize one structure may not stabilize others. Previously, we have shown that benzimidazole-carbazole conjugates selectively bind and stabilize the telomeric G quadruplex structures over B-form DNA and inhibit telomerase activity and proliferation of human cancer cells. In addition, our previous studies have shown that these ligands induce topological conversion from non-parallel to parallel forms in the human telomeric G quadruplex structure. In the present study, we have investigated the interaction of bezimidazole-carbazole ligands with c-MYC, c-KIT1, c-KIT2, VEGF and BCL2 promoter G quadruplex structures. CD measurements suggested that ligands induce topological changes from hybrid to stable parallel G-quadruplex DNA. Our CD melting and FID assays revealed that these ligands show higher affinity and confers stability to promoter G-quadruplexes. Further, to investigate the probable modes of binding of the ligands to various G4 DNAs at the promoter and telomeric regions, we have performed the docking studies, and which shows ligands interacts with promoter G-quadruplex. Overall, this study suggests that ligands that are earlier shown to interact with telomeric G-quadruplex DNA also stabilize promoter G-quadruplexes. The development of ideal anti-cancer therapies that are highly efficient and exhibit minimal systemic toxicity is an important research area. The pro-drug approach has generated significant interest for selective targeting of cancerous cells. Photodynamic therapy (PDT) is one of the novel pro-drug approaches that involve activation of the pro-drug by a light stimulus. PDT involves light and a photosensitizer (PS) that in conjunction with molecular oxygen elicits cell death. A large number of ruthenium complexes have been examined for their DNA binding properties and photo-reactivities. In the present study, we have synthesized and characterized four new ruthenium azo-8-hydroxyquinoline complexes, their DNA binding properties and anticancer activities. Our studies revealed that these complexes can be stimulated by visible light to induce ROS mediated DNA photocleavage activity in a cellular environment. Interestingly, these complexes display potent cytotoxic activity in cancer cells, which is further augmented by exposure to visible light. Thus, we propose that the new Ru-complexes have the potential to be used in photodynamic therapy and as anticancer agents. Thus, the current work not only provides new insights into the regulation of ACC1 gene expression, but also identified a promising set of ruthenium metal complexes.

Non-canonical DNA structures are involved in fundamental biological processes as replication, transcription and repair. Their dysregulation is indeed connected to the development of several human diseases, including cancer. As more and more information about their existence and function in living cells are documented, such DNA structures have emerged as promising therapeutic targets. In the last decades, the G-quadruplex folding has caught the attention of scientists because of its implication in the origin and growth of various cancer forms. The stabilization of G-quadruplex structures at human telomeres is thought to be particularly attractive as it might lead to the identification of potential drug candidates with wide-spectrum anticancer activity and reduced side effects in comparison to classical chemotherapies. The research project underlying this thesis concerns the structural investigation on the interaction of non-canonical DNA foldings, especially of the human telomeric G-quadruplex, with natural and synthetic compounds in order to select potential anticancer drugs. The characterization of ligand-DNA adducts has been carried out primarily by X-ray crystallography which provides detailed structural information. In addition, alternative techniques, as CD spectroscopy and in silico calculations, have supplied complementary data with particular reference to the formation of adducts in solution.

Folate is an essential micronutrient required for one-carbon metabolism involved in regulating DNA synthesis, DNA repair and gene expression. Dietary deficiencies in folate result in an increased uracil:thymidine ratio and cytosine hypomethylation in the genome, as well as chromosomal aberrations, the latter being a validated biomarker of cancer risk. Telomeres, the regions of DNA that cap the ends of each chromosome, are critical for maintaining chromosome stability, however, the impact of folate deficiency on telomere structure and function had not previously been investigated. It was hypothesised that the high frequency of thymidine residues in the telomeric repeating hexamer,(TTAGGG)n, may cause this region to be particularly vulnerable to damage caused by folate insufficiency, leading to accelerated telomere attrition if uracil was incorporated into DNA instead of thymidine. In vitro studies were conducted to test this hypothesis using WIL2-NS cells (a p53 deficient B-lymphoblastoid cell line), cultured in medium containing low, medium or high concentrations of folic acid (FA). A flow cytometric method was used to measure telomere length (TL) at regular time points, and these data were correlated against biomarkers of chromosomal instability (CIN) scored in the cytokinesis-block micronucleus cytome (CBMNCyt) assay (micronuclei (MNi), nuclear buds (NBuds) and nucleoplasmic bridges (NPBs)), global hypomethylation and uracil incorporation into telomeric DNA sequences. Findings in the WIL2-NS model showed a significant decline in TL over the longer term (> 14 days of culture), consistent with the hypothesis. In the short term (< 14 days of culture), however, a significant and rapid increase in TL was recorded in low FA cultures, in a dosedependent manner. Furthermore, consistent with previous literature, all biomarkers of CIN increased significantly under low FA conditions. As such, the relationship between TL and CIN was found to be significant and positive in the short term, the opposite to that hypothesised, indicating that the generation of cells with longer telomeres by FA deficiency coincided in a greater degree of CIN during this period. In exploring the mechanism underlying the rapid elongation of telomeres under low FA conditions, new evidence came to light which suggested that hypomethylation of the subtelomere may lead to increased TL. As folate is required for maintenance of DNA methylation, a new hypothesis was then proposed; that hypomethylation due to FA insufficiency results in telomere elongation. This new hypothesis was tested by culturing WIL2-NS cells in complete medium containing a DNA methyltransferase inhibitor, 5-aza-2’ deoxycytidine (5azadC). Results showed a significant, rapid increase in TL with increasing 5azadC, verifying that hypomethylation was the likely cause of telomere elongation observed in this cell type and these events also coincided with large increases in CIN biomarkers. Another novel finding arising from this project was a high frequency of cytokinesis-blocked, binucleated cells displaying multiple NPBs following culture either in low FA, or high 5azadC. New nuclear morphologies, possibly arising from the formation of multiple dicentric chromosomes, were then identified and scored as part of this study. As NPBs can be representative of fusions between chromosomes with compromised telomeres, the high frequencies of these nuclear morphologies suggest that maintenance methylation may play an important role in protecting telomere integrity. Following on from the WIL2-NS studies, peripheral blood lymphocytes (PBLs) were cultured under FA deficient conditions. Results showed that FA concentration had no impact on TL in this cell type, however, significant increases in biomarkers of CIN were observed. Again, novel nuclear morphologies, possibly due to multiple dicentric chromosome formation, were identified in PBL cells cultured under FA deficient conditions. These findings further suggested that folate deficiency may result in enhanced chromosome fusigenic potential. A final investigation was conducted to explore the in vivo relationship between TL of PBL with plasma folate (PF), vitamin B12 (B12) and homocysteine (Hcy) status, and whether any such relationship was dependent on age, gender, body mass index (BMI) and common polymorphisms in folate metabolism genes. Significant relationships were only observed in the older male subset of the cohort whereby plasma folate was found to be positively associated with shorter TL, while TL and plasma Hcy were inversely associated. Overall, the findings of these studies demonstrate that FA deficiency in vitro impacts telomeres differentially, depending on cell type and cell culture duration, and that the hypomethylating effect of low folate may impact telomere integrity indirectly possibly via hypomethylation or other unexplored mechanisms. The findings that short-term folate deficiency and DNA hypomethylation may lead to telomere elongation, in parallel with a dramatic increase in CIN, and specifically multiple NPBs, has not previously been shown. In vivo findings, however, suggest that low folate, and high Hcy, may also have an adverse impact on telomere length, particularly in older males. Most importantly, results of this study show that TL, alone, is probably inadequate and inappropriate as a sole measure of chromosomal instability, and that biomarkers of telomere structure and dysfunction, and possibly subtelomeric DNA methylation, are likely to be of considerably greater value in this context and should be considered for validation in future studies.
Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2010

Telomeres are nucleoprotein structures that protect the ends of linear chromosomes. They are composed of long tracts of TTAGGG repeats, telomere specific proteins that form the shelterin complex and several telomere accessory proteins that co-operate to telomere metabolism. Proper telomere maintenance is a crucial process to protect the genome against instability and telomere dysfunction has been linked to tumorigenesis and premature aging. AKTIP gene is the human homologue of Drosophila peo, a gene that was recently linked to telomere metabolism. The aim of this study was to understand if AKTIP could have a role in human telomere metabolism, in analogy with the telomeric function of its homologous in fly. For this purpose we have analyzed the phenotype of human cells in which AKTIP expression was downregulated by RNA interference. In human primary cells AKTIP downregulation triggered the reduction of the mitotic index, proliferation impairment and premature senescence. AKTIP reduction induced a strong DNA damage response proved by the accumulation of the phosphorylated form of proteins involved in DNA damage sensing and signaling such as ATM, p53 and Chk1, by the accumulation of p21 mRNA and by the formation of foci containing DNA damage response proteins. About half of these foci were located at telomeres (TIFs) indicating the presence of dysfunctional telomeres in AKTIP knocked down cells. These data were consistent with the accumulation of aberrant telomeres in MEFs p53-/- observed following the downregulation of murine homologue of AKTIP (named Ft1). AKTIP involvement in telomere metabolism was further suggested by its interaction with telomeric repeats observed by ChIP analysis. Altogether, these findings indicate that AKTIP takes part in telomere maintenance. Interestingly, immunostaining assays showed that AKTIP is not a stable component of telomeres but was found located in the nucleus, mainly at nuclear rim. This particular localization, in addition with the telomeric role outlined for AKTIP, suggest that AKTIP is a telomeric nonshelterin protein. Consistent with this hypothesis, we observed that Ft1 downregulation caused the formation of chromosomal aberrations in addition to telomeric abnormalities, indicating that AKTIP/Ft1 plays a role not only in telomere maintenance but also in the overall genomic stability, possibly contributing to DNA replication. Indeed, the most prominent telomeric aberration observed in Ft1 downregulated MEFs was the formation of multiple telomeric signals at the ends of chromosomes, also known as fragile telomeres, indicative of replication impairment. In addition, AKTIP downregulation was found to induce an S-phase block of cell cycle progression and a strong reduction of PCNA positive cells in primary fibroblasts, along with an increased sensitivity to drugs that impair DNA replication, as aphidicolin. Collectively, these data demonstrate that AKTIP is a protein needed for proper DNA maintenance in mammalian cells. In the telomeric context AKTIP likely is a telomeric accessory protein, rather than a shelterin-like protein, because it’s conserved in fly, differently from shelterin proteins, has a role in telomere maintenance but is not stably located at telomeres. AKTIP, in addition to its telomeric function, seems to have a more general role in cellular metabolism, as all the other telomeric nonshelterin proteins. In particular our data indicate that AKTIP could be involved in DNA replication. Considering all the collected data together, our current hypothesis is that AKTIP plays a role in replication of complex DNA structures, including telomeric repeats. Its downregulation could impair the replication fork progression through these DNA regions leading to chromosomal aberrations, DNA damage response and cell cycle alterations, the most prominent phenotypic traits of AKTIP knocked down cells.

The mammalian protein POT1 binds to telomeric single-stranded DNA (ssDNA), protecting chromosome ends from being detected as sites of DNA damage. POT1 is composed of an N-terminal ssDNA-binding domain and a C-terminal protein interaction domain. With regard to the latter, POT1 heterodimerizes with the protein TPP1 to foster binding to telomeric ssDNA in vitro and binds the telomeric double-stranded-DNA-binding protein TRF2. We sought to determine which of these functions-ssDNA, TPP1, or TRF2 binding-was required to protect chromosome ends from being detected as DNA damage. Using separation-of-function POT1 mutants deficient in one of these three activities, we found that binding to TRF2 is dispensable for protecting telomeres but fosters robust loading of POT1 onto telomeric chromatin. Furthermore, we found that the telomeric ssDNA-binding activity and binding to TPP1 are required in cis for POT1 to protect telomeres. Mechanistically, binding of POT1 to telomeric ssDNA and association with TPP1 inhibit the localization of RPA, which can function as a DNA damage sensor, to telomeres.
Dissertation