Dissertations / Theses on the topic 'Histone post-translational modifications (hPTMs)'
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GHIANI, LAVINIA. "THE HISTONE POST-TRANSLATIONAL MODIFICATION LANDSCAPE IN HPV+ AND HPV- HEAD AND NECK SQUAMOUS CELL CARCINOMA: CHARACTERIZING THE ONCOGENIC ROLE OF THE H3K36ME2 METHYLTRANSFERASE NSD2." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/820678.
Full textParameswaran, Kalaivani Nithyha. "Understanding the mechanisms of histone modifications in vivo." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAJ097/document.
Full textPost-translational modifications (PTMs) of histones have emerged as key players in the regulation of gene expression. However, little is known to what extent PTMs can directly impact chromatin. It has been suggested that PTMs of core histones (H2A, H2B, H3 and H4) have the potential to govern chromatin function according to the so called ‘‘histone code’’ hypothesis by recruiting specific binding proteins. The goal of my project is to gain insight in the function acetylation within the globular domain of H3 and to compare these modifications with histone tail modifications, in vivo by using the CRISPR in mouse embryonic stem cells (ES). To study the impact of PTMs in vivo, all endogenous wild type (WT) H3 gene copies have to be replaced with mutant copies. Hence, the primary focus of my project is to establish cell lines that exclusively express mutated H3 (e.g. mimicking acetylation) in order to study effects of H3 globular domain modifications on (a) gene expression (b) chromatin architecture as well as to study (c) cross talks and synergisms between globular domain modifications and (d) compare the effects with tail modifications in an vivo system
Bodey, Elijah D. "Evaluation of Cell Permeability of Intact Histone Complexes in Mammalian Cells." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1525705861000928.
Full textKurtz, Katryn Lucille. "Structure of chromatin, protein transitions, and post-translational histone modifications in several sperm models." Doctoral thesis, Universitat de Barcelona, 2008. http://hdl.handle.net/10803/1158.
Full textFor three different models using four marine species, protein transitions, chromatin condensation, and acetylation patterns were described during spermiogeneis. Specifically, changes in chromatin architecture and its protein complement was extensively studied using mainly transmission electron microscopy, inmunocytochemistry using anti-histone, anti-precursor protamine, and anti-acetyl group antibodies, as well as high resolution polyacrylamide gel electrophoresis (PAGE) and western blotting.
A model of specialized sperm chromatin (crustacean type) has been included in this study, since for decades this type of chromatin has remained poorly understood. Crustacean type sperm, once believed to have nuclei void of basic DNA-associated proteins, was found to contain histones, and is considered a derivation of the "H" model. Three species of brachyuran crabs from two different families were used to compositionally and ultrastructurally study this unusually decondensed mature sperm chromatin. Characterization of the histones from these sperm using HPLC and amino acid analysis confirm that the basic proteins extracted from sperm of these crabs are indeed typical and canonical histones, though some appear modified by post-translational modifications such as acetylation, which has never before been described in mature sperm. Additionally, in Maja brachydactyla, histones H3 and H2B appear in stoichiometric amounts different to what would be found in somatic chromatin. By performing micrococcal nuclease digestions, the presence of nucleosomes (or nucleosome-like particles) in the sperm of these species was confirmed, and demonstrated that histones are found interacting with the sperm DNA. Further, the histone/DNA ratio was evaluated in two Cancer species, and it was determined that these sperm only contain slightly over half the amount of basic protein per DNA unit compared to other sperm types. These results concerning the composition of the crustacean-type sperm chromatin help to explain its decondensed nature.
Minshull, Tom. "Studying the effects of severe sepsis on histone post translational modifications using mass spectrometry." Thesis, University of Sheffield, 2016. http://etheses.whiterose.ac.uk/13244/.
Full textBock, Ina [Verfasser]. "Recognition of post-translational histone modifications by antibodies and epigenetic reading domains / Ina Bock." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2013. http://d-nb.info/1037013751/34.
Full textLópez, Ramos Rita. "Linker histone post-translational modifications and effects of phosphorylation on secondary structure and chromatin aggregation." Doctoral thesis, Universitat Autònoma de Barcelona, 2013. http://hdl.handle.net/10803/131313.
Full textLinker histones play an important role in establishing and maintaining chromatin higher-order structure and in transcriptional regulation. Histone H1 in vertebrates has a characteristic three-domain structure consisting of a short flexible N-terminal domain, a central globular domain and a long C-terminal domain. The amino- and carboxyl-terminal (CTD) domains are highly basic and mainly unstructured in aqueous solution. The charge distribution is quite uniform along the CTD. Because of that, chromatin condensation is mediated through charge-neutralization of the negatively charged linker DNA, facilitating chromatin condensation into the 30nm fibre and also intermolecular aggregation. Interaction with DNA induces the complete folding of the CTD under physiological conditions in a very stable manner, which allows to classify this domain as an intrinsically disordered protein, with coupled binding and folding. Post-translational phosphorylation of the CTD of H1 has effects on secondary structure and DNA condensation. Secondary structure of the entire H10 was analysed by infrared spectroscopy. H10, as the isolated CTD, also folded upon DNA interaction and the secondary structure was modulated by phosphorylation. The structural change following phosphorylation was characterized by an increase in the amount of β‐structure that was more significant when bound to DNA and was dependant on the protein/DNA ratio. The proportion of β‐structure reached 54 % suggesting that the CTD was in an all‐β conformation in the entire protein. Concomitant with the increase in β‐structure, there was a remarkable decrease of α‐helix that suggested the loss of some of the α‐helix in the globular domain; probably associated to the propagation of the β‐structure from the CTD towards the rest of the protein. In the presence of SDS, H10 folded with percentages of secondary structure motifs similar to those found when bound to DNA. At a molar ratio 14:1 (SDS/protein) the triphosphorylated protein had 55% of β‐structure indicating that the CTD within histone H10 was also in an all‐β conformation and formed amyloid fibres. Mature chicken erythrocyte nuclei contain highly condensed and inert chromatin, mainly consisting of DNA and histone proteins. Chicken erythrocyte chromatin was used to analyse linker histones post-translational modifications and the effect of phosphorylation by CDK2 on chromatin aggregation. The nuclei were digested with micrococcal nuclease and fractionated by centrifugation in low-salt buffer into soluble and insoluble fractions. Post-translational modifications (PTMs) of the purified linker histones of both fractions were analyzed by Tandem MS. All six histone H1 subtypes (H1.01, H1.02, H1.03, H1.10, H1.1L and H1.1R) and histone H5 were identified. In our study, we identified eight novel post-translational modifications: two were identified in histone H5 and six in histone H1 subtypes. Some of the identified modifications were specific of one chromatin fraction suggesting the differential distribution of some PTMs within chromatin. Comparison of the PTMs found with other previously reported for other species showed that most of them are conserved through evolution. Since histone H1 develops its function within chromatin; chicken erythrocyte chromatin was phosphorylated ex vivo with CDK2 in the S/T-P-X-Z motifs present in linker histones in order to study the effects of ex vivo phosphorylation of linker histones on chromatin aggregation. Proteomic analyses by HPCE and MALDITOF-MS showed that the the number of phosphate groups increased with the time of phosphorylation, reaching, in the case of H5, 54% of phosphorylated species (mono and diphosphorylated) after overnight phosphorylation. Tandem MS after proteolytic digestion revealed that in all linker histones the S/T-PX-Z motifs were unphosphorylated in native chromatin indicating that the phosphorylated peptides found at other times of reaction were modified ex vivo. In H5, only S148 was identified in all samples and was phosphorylated after 1 hour. In the Tandem MS analysis of histone H1 subtypes, all the CDK2 consensus sequences, except S171(H1.1R numbering) were identified for H1.03, H1.1L and H1.1R. H1.03T16 was found phosphorylated after 15 minutes; H1.1LS192 and H1.1RS186 after 1 hour; H1.03S155, H1.1LS155 and H1.1RS153 after3 hours. Once ex vivo phosphorylation of linker histones within chromatin was confirmed, the effect of linker histones ex vivo phosphorylation on chromatin aggregation induced by MgCl2 (1.6 mM) was analysed by Dynamic Light Scattering (DLS). The most remarkable result associated to ex vivo phosphorylation of linker histones within chromatin was a decrease in the hydrodynamic diameter of the aggregated molecules. The differences became greater with the increase of phosphorylation time and with the size of the chromatin fragments. These results indicated that linker histones phosphorylation impaired chromatin aggregation.
Shahidian, Lara [Verfasser], and Robert [Akademischer Betreuer] Schneider. "The role of novel histone post-translational modifications in transcription / Lara Shahidian ; Betreuer: Robert Schneider." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2020. http://d-nb.info/1236502051/34.
Full textKarim, Muhammed. "Study of the post-translational modifications of histone H4 by Fourier transform ion cyclotron resonance mass spectrometry." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/9780.
Full textGoudarzi, Afsaneh. "Male genome programming guided by histone acylations." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAV059/document.
Full textThe main focus of the investigations reported in this manuscript is the understanding of the regulatory events that are based on histone lysine modifications in post-meiotic male germ cells, where specific and chromosome-wide regulations of gene expression occur. In the first part of my work we designed a strategy to specifically investigate the role of the histone acetyl-transferases (HATs), Cbp and p300, in post-meiotic male germ cells.Accordingly, we generated double Cbp and p300 conditional knock-out mice resulting in a partial depletion of Cbp and p300 in post-meiotic cells. Although the mice were fertile and spermatogenesis seemed to take place normally, a transcriptomic analysis of early and late post-meiotic germ cells led to the identification of a specific subset of genes with an increased expression in late spermatogenic cells that is highly sensitive to the decreased amounts of Cbp and p300. In conclusion, these results have revealed an interesting new gene expression program specific to post-meiotic male germ cells that are specifically regulated by the considered HATs.Taking into account the occurrence of a variety of histone lysine acylations, we extended these investigations to a four-carbon histone lysine modification, butyrylation. Accordingly, we have undertaken a comprehensive comparative analysis of histone H4 acetylation and butyrylation on its K5 and K8 positions in differentiating male germ cells. Genome-wide mapping of H4K5ac, H4K5bu, H4K8ac and H4K8bu at two critical developmental stages, meiotic and post-meiotic haploid cells, shows an interchangeable use of acetylation and butyrylation in the Transcriptional Start Sites (TSSs) of the most highly expressed genes in both meiotic and haploid round spermatids. Interestingly, many of these promoters are also bound by the essential regulator of spermatogenic gene expression, the BET bromodomain-containing factor, Brdt. A detailed analysis of Brdt binding capacity of H4 tails bearing various combinations of K5 and K8 acetylation and butyrylation showed that H4K5 butyrylation severely interferes with Brdt-binding. Our results therefore indicate that not only Brdt is required for the activation of a meiotic and post-meiotic gene expression program, but also its turnover induced by H4K5 butyrylation is equally important. This work hence highlights how an interplay between two different acylations occurring on the same lysines can play an essential regulatory role by increasing the chromatin binding dynamics of a critical lysine acetyl-reader, Brdt.Finally, in a collaborative work with structural biologists we showed that while p300 is a robust acetylase, its activity gets weaker with increasing acyl chain length. These results suggest that in vivo, p300 would use a specific co-factor to ensure non-acetyl histone acylations.Overall, these investigations shed an important light on how the male genome programming is guided by histone acylations and revealed for the first time a molecular network that regulates histone acylations and mediates its functional impact
Mooney, Alex M. "The Influence of DNA Sequence and Post Translational Modifications on Nucleosome Positioning and Stability." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354733493.
Full textMartínez, Cebrián Gerard 1992. "Identification of novel histone marks required for the transcriptional stress response." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/668153.
Full textDurant estressos ambientals, com ara fluctuacions de temperatura o augment de l'osmolaritat, el llevat Saccharomyces cerevisiae indueix una reprogramació transcripcional per sobreviure i adaptar-se a l'estrès. Les modificacions post-traduccionals d'histones són elements reguladors clau coneguts per modular la transcripció. Utilitzant una col·lecció complet de mutants d'histona, vam realitzar un cribratge transcripcional a gran escala per a avaluar els residus d'histona necessaris per a una inducció adequada de senyalitzadors fluorescents que responen a estrès osmòtic i tèrmic. Del nostre cribratge, vam poder extreure conclusions generals sobre els residus d'histona necessaris per a la transcripció induïda per estrès. Vam observar poc solapament entre els residus necessaris per l’estrès tèrmic i osmòtic. Els resultats del cribratge també suggereixen que els residus accessibles i modificables, quan se’ls mutava, eren més propensos a afectar la transcripció induïda per l'estrès. Seguint aquestes indicacions, vam seleccionar els residus accessibles i modificables H4-S47 i H4-T30 ja que la seva mutació proporcionava defectes transcripcionals en estrès osmòtic i tèrmic respectivament. Vam validar i caracteritzar l’extensió dels seus defectes transcripcionals mitjançant norther blot i seqüenciació d’ARN. També vam identificar i caracteritzar Cla4 i Ste20 per a H4-S47 i Ste11 per a H4-T30 com a possibles quinases que fosforilen els dos residus en estrès. A més, l'estudi d'altres residus identificats en el cribratge obre noves possibilitats per identificar noves modificacions d'histona rellevants per a la resposta transcripcional en estrès.
Pengelly, Ana R. [Verfasser], and John [Akademischer Betreuer] Parsch. "Functional analysis of histone post-translational modifications by the polycomb group of transcriptional repressors / Ana R. Pengelly ; Betreuer: John Parsch." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1114068136/34.
Full textPengelly, Ana Raquel [Verfasser], and John [Akademischer Betreuer] Parsch. "Functional analysis of histone post-translational modifications by the polycomb group of transcriptional repressors / Ana R. Pengelly ; Betreuer: John Parsch." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1114068136/34.
Full textContrepois, Kévin. "Modifications de la chromatine associées à la sénescence cellulaire." Thesis, Paris 11, 2012. http://www.theses.fr/2012PA112102.
Full textCellular senescence is a stress response of mammalian cells characterized by a stable cell proliferation arrest. It can be triggered by telomere dysfunction, genotoxic stress and oncogene activation. Cellular senescence acts as a natural barrier against cancer development and is involved in ageing. Senescent cells reorganize their genome by the assembly of chromatin into senescence-associated heterochromatin foci (SAHF). We showed that SIRT2-mediated global deacetylation of H4-K16Ac is involved in heterochromatin assembly in senescence. Moreover, we identified the accumulation with time of specific H2A and H2B variants in senescence triggered by persistent DNA damage signaling. These histone variants could have specific functions in senescent cells and could be a useful ageing biomarker in vivo.This work provides novel insights into chromatin modification and epigenetic regulation in cellular senescence
Bilgraer, Raphaël. "Déchiffrer le code histone : épigénétique et toxicologie placentaire." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05P627/document.
Full textWhile acting upon chromatin compaction, histone post-translational modifications (PTMs) are involved in modulating gene expression through histone–DNA affinity and protein–protein interactions. These dynamic and environment-sensitive modifications are constitutive of the histone code that reflects the transient transcriptional state of the chromatin. Here we describe a global screening approach for revealing epigenetic disruption at the histone level. This original approach enables fast and reliable relative abundance comparison of histone PTMs and variants in human cells within a single LC-MS experiment. As a proof of concept, we exposed BeWo human choriocarcinoma cells to sodium butyrate (SB), a universal histone deacetylase (HDAC) inhibitor. Histone acide xtracts equally representing 3 distinct classes, Control, 1 mM and 2.5 mM SB, we reanalyzed using ultra-performance liquid chromatography coupled with a hybrid quadrupoletime-of-flight mass spectrometer (UPLC-QTOF-MS). Multivariate statistics allowed us to discriminate control from treated samples based on differences in the acetylation level of several histone forms. We then applied the same procedure to cells treated with 1 μMB[a]P and suceeded in revealing two markers of chromatin remodeling in relation withgenotoxic properties of B[a]P. Indeed, this untargeted histonomic approach could be auseful exploratory tool in many cases of environmental xenobiotic exposure when histone code disruption is suspected
Soldi, M. "ESTABLISHMENT AND OPTIMIZATION OF THE CHROP APPROACH, COMBINING CHIP AND MS-BASED PROTEOMICS, FOR THE CHARACTERIZATION OF THE CHROMATOME AT DISTINCT FUNCTIONAL DOMAINS." Doctoral thesis, Università degli Studi di Milano, 2013. http://hdl.handle.net/2434/219069.
Full textJordi, Emmanuelle. "Histone post-translational modifications in the nuclei of striatal D1 and D2 neurons : development of a novel method of study and effects of cocaine." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2012. http://tel.archives-ouvertes.fr/tel-00831656.
Full textMcKee, Christopher J. "Characterizing interactions of HIV-1 integrase with viral DNA and the cellular cofactor LEDGF." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1274979614.
Full textBernier, Morgan Welsh. "The Structure of Chromatin and its Influence on Gene Regulation." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1417617602.
Full textMonneau, Yoan. "Etude des modifications post-traductionnelles des histones : l’analyse structuro-fonctionnelle d'une peptidyl-prolyl isomérase et la production semi-synthétique d’une protéine acétylée." Thesis, Bordeaux 2, 2011. http://www.theses.fr/2011BOR21900/document.
Full textThe structural unit of chromatin, the nucleosome, is composed of double-stranded DNA wrapped around a histone octamer and is subject to a plethora of post-translational modifications. The biological consequences of peptidyl-prolyl isomerization and lysine acetylation were investigated at atomic scale through analysis of in vitro reconstituted systems by NMR. Peptidyl-prolyl bonds of histone H3 N-terminal domain are substrates in vitro of an isomerase from S. cerevisiae named Fpr4p, which underlies transcriptional control dependent on its catalytic activity. The solution structure of the catalytic domain of Fpr4p was calculated based on restraints from NMR spectroscopy, and reveals a canonical catalytic domain belonging to the FK506-binding protein (FKBP) family. Based on primary sequence analysis and NMR experiments, a preliminary structural model of full length Fpr4p is also presented. Functional analyses were performed with three decapeptides designed from the primary sequence from the N-terminal tail of S. cerevisiae histone H3. All three constitute substrates of Fpr4p, with equivalent catalysis observed for Pro16 and Pro30. The equilibrium proportion of the cis-proline conformer has been determined for all three decapeptides, and these populations are unaffected by Fpr4p catalytic activity. Structural ensembles of the substrates with proline in the trans conformation were determined by using NMR spectroscopy, and will be subsequently used for in silico molecular docking onto Fpr4p. To study a second form of histone regulation, a semi-synthetic method to produce acetylated protein was developed. The protocol relies on the site-specific mutation of lysine to cysteine in recombinant proteins followed by controlled alkylation thanks to nucleophilicity of the introduced thiol. The production of the required alkylation reagent is easy, quick, and suitable for biology laboratory and allows diverse isotopic labeling within the acetyl group. Alkylation of folded proteins has also been achieved in native conditions. As one target of acetylation in vivo, the histone H2A-H2B dimer is an intermediate of nucleosome assembly and was reconstituted in vitro. Chemical shift values of the N- and C-terminal domains of H2A are in agreement with an intrinsically disordered state although they display differences in dynamic mobility
Studencka, Maja [Verfasser], Monika [Akademischer Betreuer] Jedrusik-Bode, Sigrid [Akademischer Betreuer] Hoyer-Fender, Michael [Akademischer Betreuer] Kessel, and Detlef [Akademischer Betreuer] Doenecke. "The influence of post-translational modifications on biology of the linker histone HIS-24 in Caenorhabditis elegans / Maja Studencka. Gutachter: Sigrid Hoyer-Fender ; Michael Kessel ; Detlef Doenecke. Betreuer: Monika Jedrusik-Bode." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2012. http://d-nb.info/1042846014/34.
Full textStudencka, Maja Verfasser], Monika [Akademischer Betreuer] Jedrusik-Bode, Sigrid [Akademischer Betreuer] Hoyer-Fender, Michael [Akademischer Betreuer] Kessel, and Detlef [Akademischer Betreuer] [Doenecke. "The influence of post-translational modifications on biology of the linker histone HIS-24 in Caenorhabditis elegans / Maja Studencka. Gutachter: Sigrid Hoyer-Fender ; Michael Kessel ; Detlef Doenecke. Betreuer: Monika Jedrusik-Bode." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2012. http://d-nb.info/1042846014/34.
Full textPratx, Loris. "Identification de marques épigénétiques chez le nématode à galles parasite de plantes Meloidogyne incognita." Thesis, Université Côte d'Azur (ComUE), 2017. http://www.theses.fr/2017AZUR4026/document.
Full textMeloidogyne incognita is the most damaging plant-parasitic nematode in agriculture. M. incognita reproduces in an asexual way by obligatory parthenogenesis. Genetically identical individuals develop from females and form clonal populations. Although these clones share the same genetic heritage, modifications of their phenotype can be observed when they are exposed to unfavorable environments. This phenotypic plasticity is characterized through two phenotypes of interest: sex-differentiation and virulence (i.e. capacity to parasite a resistant crop). Sex-differentiation varies among environmental conditions and was reported to be linked to decondensed chromatin regions. Virulence is an heritable character transmitted in a non-Mendelian way. Our study focuses on identifying the role of epigenome in the generation of phenotypic variability. To this end we detailed the presence of proteins involved in epigenetic regulations in Meloidogyne spp. We also developed a ChIP-seq assay to compare histone modifications between different developmental stages and between virulent and avirulent parasites. Our results allow to detect specific histone patterns associated with M. incognita development. These results lead us to propose a model that could explain sex determination in M. incognita. We also could link virulence acquisition with the loss of some specific genomic regions that contains more than 300 genes including already described potential avirulence factors. This study opens the way for analyzing the role of epigenetic mechanisms at a whole genome scale, and allows to identify novel biological processes involved in phenotypic variation in asexual organisms
David, Sarah-Anne. "Impact de l'acclimatation embryonnaire à la chaleur sur des modifications post-traductionnelles des histones chez le poulet." Thesis, Tours, 2017. http://www.theses.fr/2017TOUR4036.
Full textPerinatal environment changes may alter gene expression throughout life via epigenetic modifications. A strategy to improve thermal tolerance of heat-sensitive chickens is a thermalmanipulation during embryogenesis (TM). During a heat challenge at the end of the rearing period (D35), modifications of gene expression have been reported in thermally-manipulated chickens. These alterations could be linked to epigenetic modifications induced during the TM that persist throughout life. This work focused on two histone post-translational modifications (HPTM): H3K27me3 and H3K4me3. We adjusted two methods of chromatin immunoprecipitation to conduct a whole genome study of these HPTM at D35, in the hypothalamus and skeletal muscle. We demonstrated that the TM has a major impact in the hypothalamus, especially on H3K4me3. These alterations seem to modulate the hypothalamic morphogenesis and its response to hormones, therefore possibly contributing to better adaptive capacities of TM chickens
Sigismondo, G. "CHROP APPROACH DISSECTS THE DYNAMIC PROFILING OF CHROMATOME AT ENHANCERS OF INFLAMMATORY GENES." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/264906.
Full textMollah, Sahana. "Analysis of histone post-translational modifications by mass spectrometry /." 2004. http://wwwlib.umi.com/dissertations/fullcit/3149142.
Full textUeberheide, Beatrix Magdalena. "Decoding the histone code : analysis of histone post-translational modifications by mass spectrometry /." 2005. http://wwwlib.umi.com/dissertations/fullcit/3177509.
Full textRocha, Rafael Amorim. "Histone post-translational modifications and chromatin remodelers in colorectal cancer." Master's thesis, 2017. https://repositorio-aberto.up.pt/handle/10216/109416.
Full textRocha, Rafael Amorim. "Histone post-translational modifications and chromatin remodelers in colorectal cancer." Dissertação, 2017. https://repositorio-aberto.up.pt/handle/10216/109416.
Full textAbshiru, Nebiyu. "Quantitative proteomics methods for the analysis of histone post-translational modifications." Thèse, 2015. http://hdl.handle.net/1866/13563.
Full textHistones are highly conserved, basic proteins found in eukaryotic cell nuclei. They organize and package DNA strands into nucleosome core particles (NCPs), the fundamental repeating units of eukaryotic chromatin. The histones are subject to a wide variety of posttranslational modifications (PTMs) including acetylation, methylation and phosphorylation. These PTMs play an essential role in DNA-replication, transcription, and chromatin assembly. Alterations in histone PTM abundances have been implicated in several types of cancer. For example, the global loss of trimethylation at H4K20 and acetylation at H4K16 is a hallmark of human cancers. Thus, characterization of histone PTMs and their dynamics is extremely useful for elucidating normal cellular functions and molecular pathways that lead to diseases. Traditionally, histone PTMs are analyzed using antibody-based approaches such as western blot and chromatin immunoprecipitation (ChIP) assays. These methods, however, suffer from several limitations including antibody cross-reactivity, epitope occlusion, and the cost and difficulty in producing and validating antibodies. Over the last decade, mass spectrometry (MS) has emerged as a powerful technique for the characterization and quantification of histone PTMs. MS offers several advantages over the traditional approaches including reproducibility, specificity, and ability to rapidly analyze numerous PTMs in a single experiment. In this thesis, the development and applications of novel analytical tools for the identification and quantification of histone PTMs are presented. First, a method useful for measuring the global and site specific changes in histone acetylation is described. This method combines intact mass analysis and peptide sequencing approaches to study the global and site specific changes in histone acetylation during in vitro assays with yeast Rtt109 and its chaperone (Asf1 or Vps75). Second, a method for analysis of isomeric histone peptides is presented. This method combines a high resolution LC-MS/MS with a novel bioinformatics tool called Iso-PeptidAce to deconvolute mixed spectra of co-eluting isomeric peptides. We benchmarked Iso-PeptidAce using mixtures of synthetic isomeric peptides. We demonstrated its capability in histones isolated from human erythroleukemic (K562) cells treated with clinically relevant histone deacetylase inhibitors (HDACi) and in affinity-purified S. cerevisiae histones bound to chromatin assembly factor-1 (CAF-1). Third, by employing the above methods, an in-depth quantitative analysis of the substrate specificities of several fission yeast HATs and HDACs was assessed. We determined the acetylation site occupancy of multiple lysines in histones isolated from a control or mutant strains lacking specific HAT or HDAC activities. Our analysis identified several known and novel HAT and HDAC target sites. Our data also defined the division of labor between the different HATs and HDACs in maintaining the steady-state level of histone acetylation. Overall, we anticipate that the methods described in this thesis will address some of the existing challenges facing the chromatin field. Moreover, the data presented will provide valuable insights for future genetic and biochemical studies involving the fission yeast.
Tabet, Sara. "Development of fluorescence-based supramolecular tools for studying histone post-translational modifications." Thesis, 2014. http://hdl.handle.net/1828/5316.
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Beisel, Nadine. "Patterns of post-translational histone modifications, chromatin condensation and DNA fragmentation during apoptosis." Doctoral thesis, 2005. http://hdl.handle.net/11858/00-1735-0000-0006-ABBA-9.
Full text"Histone post-translational modifications in the brain of the senescence-accelerated prone 8 mouse." Thesis, 2009. http://library.cuhk.edu.hk/record=b6074980.
Full textNowadays, many countries including China are experiencing aging populations. Aging has become the major risk factor for many diseases, such as neurodegenerative disease. The studies on the role of epigenetics in the aging process have grown tremendously in recent years. However, no systematic investigations have provided the information on histone post-translational modifications (PTMs) in aged brain and the roles of histone PTMs in brain aging are still unknown.
This study gave a new insight into the link between histone PTMs and brain aging. It could provide the experimental evidence for future studies and help us to better understand aging or neurodegenerative disease at epigenetic level. Furthermore, it could benefit for setting up the strategies for epigenetic therapy to neurodegenerative disease.
Wang, Chunmei.
Adviser: Ngai Saiming.
Source: Dissertation Abstracts International, Volume: 73-01, Section: B, page: .
Thesis (Ph.D.)--Chinese University of Hong Kong, 2009.
Includes bibliographical references (leaf 136).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Abstract also in Chinese.
Beisel, Nadine [Verfasser]. "Patterns of post-translational histone modifications, chromatin condensation and DNA fragmentation during apoptosis / vorgelegt von Nadine Beisel." 2006. http://d-nb.info/982205414/34.
Full textStudencka, Maja. "The influence of post-translational modifications on biology of the linker histone HIS-24 in Caenorhabditis elegans." Doctoral thesis, 2012. http://hdl.handle.net/11858/00-1735-0000-000D-EF62-1.
Full textPesavento, James J. "Improved dynamic range, quantitation, and characterization of histone H4 post-translational modifications : a top down mass spectrometric approach /." 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3223689.
Full textSource: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3643. Adviser: Neil L. Kelleher. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.
Draker, Ryan. "A Characterization of the Role of Post-translational Modification in Transcriptional Regulation by the Histone Variant H2A.Z." Thesis, 2012. http://hdl.handle.net/1807/33981.
Full textDrogaris, Paul. "Analytical strategies for the comprehensive profiling of histone post translational modifications by mass spectrometry and implications for functional analyses." Thèse, 2010. http://hdl.handle.net/1866/4934.
Full textIn eukaryotic cells, the lengthy DNA biopolymer is condensed into the cell nucleus with the aid of small packaging proteins called histones. In addition to their packing functions,histones are also targets of numerous post translational modifications (PTMs), especially on their N-terminus. These reversible modifications are believed to be constituents of a heritable epigenetic “histone code” that dynamically orchestrate and modulate chromatin based events such as gene activation and silencing, DNA replication and repair, and are also involved in the downstream signaling and progression of cancers, such as leukemia. Thus, the elucidation of histone PTMs is important in understanding their biological function. An analytical workflow was designed and set-up in the laboratory to isolate, detect, and quantitate histone PTM, using a two-pronged, unbiased, and rapid approach with specialized bioinformatic tools. The workflow was validated using histones from wildtype, and 2 mutants deficient in acetyltransferase activity. Between the three histone sources, the only PTM that demonstrated any change was acetylation at histone H3 lysine 56 (H3K56ac). The down-regulation and stoichiometry of this PTM was accurately assessed between wild-type and mutant cells. The versatile scan functions of a hybrid quadrupole-linear ion trap instrument were exploited to enhance the detection of intact histone proteins. The enhanced multiply charged (EMC) scan was modified in order to contain and detect intact protein ions within the linear ion trap. This targeted EMC (or tEMC) resulted in not only a 4-fold increase in signal-to-noise, but also a 5-fold increase in resolution. Furthermore, the charge separation capability of the tEMC dramatically reduced space charge effects within the linear ion trap. The superior resolution of the tEMC mode allowed for the discimination of many modified histone isoforms, especially for histone H3. Using the bottom-up strategy with multiple reaction monitoring (MRM), histone peptides were quantified and sequenced with a high degree of precision. The only PTM that was down-regulated between wild-type and DOT1L mutant histones was methylation at histone H3 lysine 79 (H3K79me1). The effects of two clinically relevant small molecule HDAC inhibitors (HDACi) on histone PTMs patterns were assessed using the analytical workflow developed. Histones derived from both normal and cancer cells were exposed to either Vorinostat (SAHA) or Entinostat (MS-275) over a 24- to 72 hour period. The two core histones primarily affected were H3 and H4. Surprisingly, the same effects were not observed when normal cells were treated with three doses of SAHA at 24-hour intervals over a 72-hour period. An absolute quantitation method using a calibration curve was developed for H3K56ac. In opposition to other published literature, our findings demonstrate that this PTM is present in very low stoichiometry (< 0.1%) in mammalian cells, and exhibits no significant up-regulation in different cell lines treated with several types of HDACi.
Dudková, Barbora. "Role paternálního H4K12ac při utváření pronukleí a v časné embryogenezi u myší." Master's thesis, 2013. http://www.nusl.cz/ntk/nusl-321094.
Full textNersesian, Jeanet. "Role of Histone H3 Lysine 56 Acetylation in the Response to Replicative stress." Thèse, 2017. http://hdl.handle.net/1866/19416.
Full textIn Saccharomyces cerevisiae, histone H3 lysine 56 acetylation (H3K56ac) occurs on all newly synthesized histones H3 that are deposited behind DNA replication forks. H3K56ac plays critical role in chromatin assembly during DNA replication and repair. H3K56ac is also required for genome stability and stabilization of stalled replication fork. Cells lacking H3K56ac are sensitive to methyl methane sulfonate and other drugs that cause replicative stress. In this thesis, we investigated the links between the replisome protein Ctf4 and the H3K56 acetyltransferase Rtt109. Deletion of CTF4 partially rescued the sensitivity of rtt109Δ cells to methyl methane sulfonate. Genetic analyses also showed that Ctf4, Rtt109, and the Rtt101-Mms1-Mms22 complex act in the same pathway to response to replicative stress. ctf4Δ and rtt109Δ cells displayed intense foci of the single-stranded DNA binding complex RPA during replicative stress, suggesting formation of excess single-stranded DNA regions at stalled replication forks, leading to hyper activation of DNA damage checkpoints. These mutants accumulated anaphase bridges and persistent foci of the homologous recombination proteins Rad51 and Rad52 in response to genotoxins, suggesting that abnormal DNA structure formed at stalled replisome may compromise their recovery. Deletion of HR genes (RAD51, RAD52, RAD54, RAD55 and MUS81) together with ctf4Δ and rtt109Δ presents synergistic sensitivity to MMS, suggesting that H3K56ac deficient cells use HR to repair the damages caused by replicative stress. Overall our results demonstrate that H3K56ac deficient cells cannot recover MMS- induced damages because HR is compromised in these mutants.
Barbour, Haithem. "Un nouveau mécanisme de régulation des complexes épigénétiques BAP1/ASXLs par ubiquitination." Thèse, 2019. http://hdl.handle.net/1866/23517.
Full textUbiquitination is a post-translational modification of proteins that involves covalently attaching the ubiquitin moiety to the lysine residues of the target protein. This modification has been reported to have a significant impact on the function, localization and stability of these targets. Once established by enzymes called E3 ligases, ubiquitination can be removed by specific enzymes called deubiquitinases, thus modulating the effects caused by this modification. BAP1 (or BRCA1-Associated Protein1) is a deubiquitinase, from the UCH (Ubiquitin C-terminal Hydrolases) family, that was originally identified as a partner of the BRCA1 (BReast Cancer Associated gene 1) tumor suppressor. We and other research groups have shown that BAP1 is associated with other co-factors forming a multi-protein complex involved in several cellular processes such as gene transcription, chromatin regulation, cell cycle regulation and DNA damage response. The major target of BAP1 is ubiquitinated histone H2A, a histone mark that has been frequently associated with a repressive chromatin conformation. What are the mechanisms regulating the BAP1 complex allowing it to perform its biological functions? Does this involve post-translational modifications affecting BAP1 partners? These questions are still incompletely answered. Thus, the objectives of our studies are to characterize the mechanism and the function of the BAP1 complex by studying the post-translational modifications that could affect its obligate partners including ASXLs. To address these questions, we studied the post-translational modifications affecting BAP1 and its two mutually exclusive co-factors ASXL1 and ASXL2 (Additional Sex Comb-like 1,2). We demonstrated that ASXL1 and ASXL2 are mono-ubiquitinated only when associated with BAP1. Taking into account that the BAP1/ASXLs complexes are highly conserved during evolution, we also demonstrated that the mono-ubiquitination of ASXLs is important for Drosophila development. Using RNAi and CRISPR/Cas9 gene depletion methods and loss-of-function mutants of BAP1 and ASXL2, we identified the precise site of ASXLs ubiquitination, the enzymes responsible for establishing this mono-ubiquitination as well as its effect on catalytic activity of BAP1. On the other hand, we investigated Drosophila development as well as human cell cycle progression to identify the biological function of ASXLs mono-ubiquitination. Our results indicate that the mono-ubiquitination of ASXL2 on lysine 370 in the presence of BAP1 is a conserved post-translational modification catalyzed directly by the UBE2E family of ubiquitin-conjugating enzymes (UBE2E1, 2, 3 in mammals and UbcD2 in Drosophila). This mono-ubiquitination event stimulates the catalytic activity of BAP1 in mammals and its Drosophila ortholog Calypso towards H2Aub in vivo and in vitro. Blocking the mono-ubiquitination of ASXLs, by mutations targeting lysine K370, induces an inhibition of BAP1 catalytic activity causing a deregulation of human cell cycle progression and a haltere-to-wing homeotic transformation in Drosophila. In addition, we were able to assess the importance of ASXLs mono-ubiquitination in cancer using the mesothelioma tumor model, demonstrating a strong correlation between the expression of BAP1/ASXL2 and UBE2Es. Our results indicate the importance of post-translational modifications, including mono-ubiquitination, in the regulation of the function and stability of the BAP1 complex. Moreover, we describe a novel mechanism of activation of a deubiquitinase by the mono-ubiquitination of its co-factor. Further studies will be needed to shed more light on the link between BAP1/ASXLs activation by mono-ubiquitination and the tumor suppressor function of BAP1 via H2Aub deubiquitination. On the other hand, we have noticed that the depletion of PSMD14, a deubiquitinase associated with the proteasome regulatory particle, induces not only a drastic reduction of H2Aub in the cell, but also rapid cell death. This prompted us initially to investigate the involvement of the catalytic activity of the proteasome in the regulation of H2Aub in connection with cell death. Although we did not find a direct link between PSMD14 and H2Aub deubiquitination, we identified several candidates (DUBs and E2s) involved in the induction of cell death while overcoming acquired resistance against proteasome catalytic inhibitors. These candidates may represent attractive targets for developing specific inhibitors to counteract resistance to proteasome inhibitors.
Daou, Salima. "Étude fonctionnelle d’un nouveau complexe multi-enzymatique régulant l’épigénome." Thèse, 2015. http://hdl.handle.net/1866/15975.
Full textThe reverse reaction of ubiquitination, a crucial post-translational modification, is catalyzed by deubiquitinases (DUBs). BAP1 is an ubiquitously expressed nuclear DUB that recently emerged as an important tumor suppressor highly mutated and inactivated in an increasing number of cancers of diverse origins. Both somatic and germline mutations with loss of heterozygosity were observed in tumors, making BAP1 the most mutated DUB in human malignancies. We previously reported that BAP1 is a component of a large multi-protein complex that includes several transcription regulators. The Drosophila homologue of BAP1, Calypso, forms the Polycomb-repressive DUB (PR-DUB) complex with Additional Sex Comb, ASX. This complex catalyzes the deubiquitination of histone H2A, an essential chromatin modification that regulates gene expression. Despite the ever increasing number of findings describing the occurrence of BAP1 mutations in cancers, few studies investigated the mechanisms of action of this DUB as a tumor suppressor. Therefore, the biological function and the mechanism of action and regulation of BAP1 remains largely uncharacterized. In the work described in this thesis, we investigated the roles of BAP1 partners in modulating its catalytic activity and tumor suppressor function. More specifically we discovered a unique mechanism of regulation between two major components of BAP1 complexes, namely HCF-1 and OGT. Indeed, HCF-1 is important for the maintenance of the cellular levels of OGT. OGT, in turn, is required for the proper proteolytic maturation of HCF-1 by promoting its O-GlcNAcylation. This signaling event is required for HCF-1 function as a cell cycle regulator. On the other hand, we deciphered an intricate mechanism of regulation of BAP1 by the atypical E2/E3 ligase, UBE2O. UBE2O, promote the multi-monoubiquitination of BAP1 on its NLS mediating its cytoplasmic sequestration and thus inhibition of its tumor suppressor function. Another aspect of modulation of BAP1 H2Aub catalysis is provided by the association of BAP1 with ASXL1 and ASXL2 (ASXL1/ASXL2), two orthologs of ASX. We investigated the role of BAP1/ASXL1/2, particularly in the mechanisms of deubiquitination and tumor suppression. We have demonstrated that BAP1 interacts directly via its C-terminal domain with the ASXM domain of ASXL1/2, thus forming two mutually exclusive complexes. Significantly, ASXM promote, through assembly with BAP1, the generation of a composite ubiquitin binding domain (CUBI), indispensable for inducing the deubiquitinase activity of BAP1 towards H2Aub. The interactions between BAP1 and ASXL1/2 regulate cell cycle progression. In addition, overexpression of BAP1 or ASXL2 in fibroblasts induces senescence in CTD- and ASXM-dependent manner. We also identified cancer-derived mutation of BAP1 that selectively abolish its interaction with ASXL1 and ASXL2 as well as its H2A deubiquitinase activity. Significantly, this mutant suppressed senescence induced by BAP1 overexpression. Thus we provided a link between the tumor suppressor BAP1, its deubiquitinase activity and the control of cell proliferation.