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Al-Ajmi, Kawthar, Shyam S. Ganguly, Adil Al-Ajmi, Zahid Al Mandhari, and Mansour S. Al-Moundhri. "Insulin-Like Growth Factor 1 Gene Polymorphism and Breast Cancer Risk among Arab Omani Women: A Case-Control Study." Breast Cancer: Basic and Clinical Research 6 (January 2012): BCBCR.S9784. http://dx.doi.org/10.4137/bcbcr.s9784.
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Breast cancer is the most common cancer worldwide with significant global burden. Insulin-like growth factor 1 (IGF1) is an important regulator of cellular growth, differentiation, and apoptosis and mitogenic and antiapoptotic activities. Some studies suggested an association between cytosine adenine (CA) repeats gene polymorphisms of IGF1 and the risk of developing breast cancer while other studies did not find such an association. This study aims investigate the role of IGF1 (CA) repeats gene polymorphisms in the risk of developing breast cancer among Omani women. Methods We analyzed (CA) repeats gene polymorphisms of IGF1 by extraction of genomic DNA from the peripheral blood of 147 patients with breast cancer and 134 control participants and performed genotyping using DNA sequencing. Results Approximately 46% of patients carried the IGF (CA)19 repeat allele, with 31.3% carrying two copies of this allele and 50% of controls carried the IGF (CA)19 repeat allele with 30.1% carrying two copies of this allele. The difference of the IGF CA repeat groups was significant between cases and controls with ( P = 0.02). In contrast, there was no difference in the distribution of (CA)19 repeat allele, (CA)18 repeat allele and (CA)19 repeat allele between cases and controls. The difference of the CA groups was significant between cases and controls among postmenopausal women with ( P = 0.026), whereas no difference was observed among postmenopausal subjects ( P = 0.429). In both pre- and postmenopausal groups there was no difference in the distribution of (CA)19 repeat allele, (CA)18 repeat allele and (CA)20 repeat allele between patients and control subjects. On further IGF1 genotypes classification, we found an association between progesterone receptor status and the genotypes group where the non carrier of (CA)19 repeat group was compared to (CA)19 repeat carrier group (OR = 2.482; 95% CI = 1.119–5.503; P value = 0.023). Conclusion Overall there was no association between the IGF (CA)19 repeat and breast cancer in Omani females.
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Han, S. W., T. Y. Kim, K. W. Lee, D. Y. Oh, S. H. Lee, D. W. Kim, D. H. Chung, S. A. Im, D. S. Heo, and Y. J. Bang. "EGFR mutation and intron 1 CA repeat polymorphism as predictive markers of gefitinib responsiveness in non-small cell lung cancer (NSCLC)." Journal of Clinical Oncology 24, no. 18_suppl (June 20, 2006): 7173. http://dx.doi.org/10.1200/jco.2006.24.18_suppl.7173.
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7173 Background: EGFR mutation is significantly associated with objective response and prolonged survival in NSCLC patients treated with gefitinib. However, presence of mutant nonresponses and nonmutant responses mandates investigation of other molecular markers for more effective prediction of gefitinib sensitivity in NSCLC. It is unclear whether low CA repeat number in EGFR intron 1 has such a predictive role. Methods: Advanced NSCLC patients received gefitinib 250mg/day. EGFR mutation in exons 18 - 21 were identified by direct sequencing of PCR products of DNA extracted from archival paraffin embedded tissue. Number of CA repeat in intron 1 of EGFR was determined by GeneScan with tumoral DNA. Baseline characteristics, mutational status, CA repeat number and efficacy of gefitinib were analyzed in respect to each other. Results: To date, 73 patients were evaluable for EGFR mutation, CA repeat and gefitinib responsiveness. 14 patients (19.2%) harbored EGFR mutation (7 deletion in exon 19, 4 L858R, 1 L861Q, 1 G719A, and 1 insertion in exon 20). Most common CA repeat genotype was 20/20 repeat (31 patients) followed by 16/20 repeat (15 patients). Patients were classified as having either low CA repeat (sum of both allele ≤ 37 repeats) or high CA repeat (≥ 38 repeats). 34 patients (46.6%) had low repeat, whereas 39 patients (53.4%) had high repeat. Patients with EGFR mutation showed better objective response (response rate [RR] 57.1% vs. 10.2% in wild type [WT], p < 0.001), time-to-progression (TTP) (p = 0.031, median 5.1 vs. 1.9 months in WT), and overall survival (OS) (p = 0.051, median14.5 vs. 7.4 months in WT). In the whole study population, low CA repeat was not associated with RR (p = 0.38), TTP (p = 0.15), or OS (p = 0.51). However, in the 59 patients without an EGFR mutation, patients with low CA repeat tended to have better objective response (RR 17.2% [5/29] in low repeat vs. 3.3% [1/30] in high repeat, p = 0.10) and significantly better TTP (p = 0.019, median 2.2 months in low repeat vs. 1.2 months in high repeat). Conclusions: Our results suggest that low number of CA repeats in EGFR intron 1 may have possible role in prediction of gefitinib responsiveness when analyzed together with EGFR mutational status. [Table: see text]
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Chhatbar, Kashyap, John Connelly, Shaun Webb, Skirmantas Kriaucionis, and Adrian Bird. "A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2." Life Science Alliance 5, no. 12 (September 19, 2022): e202201522. http://dx.doi.org/10.26508/lsa.202201522.
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The DNA-binding protein MeCP2 is reported to bind methylated cytosine in CG and CA motifs in genomic DNA, but it was recently proposed that arrays of tandemly repeated CA containing either methylated or hydroxymethylated cytosine are the primary targets for MeCP2 binding and function. Here we investigated the predictions of this hypothesis using a range of published datasets. We failed to detect enrichment of cytosine modification at genomic CA repeat arrays in mouse brain regions and found no evidence for preferential MeCP2 binding at CA repeats. Moreover, we did not observe a correlation between the CA repeat density near genes and their degree of transcriptional deregulation when MeCP2 was absent. Our results do not provide support for the hypothesis that CA repeats are key mediators of MeCP2 function. Instead, we found that CA repeats are subject to CAC methylation to a degree that is typical of the surrounding genome and contribute modestly to MeCP2-mediated modulation of gene expression in accordance with their content of this canonical target motif.
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Ishimitsu, Toshihiko, Kazuyoshi Hosoya, Kohju Tsukada, Junichi Minami, Megumi Teranishi, Mayumi Saitoh, Miki Nakamura, Yasuo Futoh, Hidehiko Ono, and Hiroaki Matsuoka. "Microsatellite DNA Polymorphism of Human Adrenomedullin Gene in Normotensive Subjects and Patients with Essential Hypertension." Hypertension 36, suppl_1 (October 2000): 715. http://dx.doi.org/10.1161/hyp.36.suppl_1.715-a.
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P121 Objective: Adrenomedullin (AM) is a hypotensive peptide widely produced in the cardiovascular organs and tissues such as the heart, kidney and the vascular cells. We investigated the association between DNA variations in AM gene and the predisposition to essential hypertension. Methods: We have cloned and sequenced the genomic DNA encoding human AM gene, and determined that the gene is located in the short arm of chromosome 11. The 3’-end of the gene is flanked by the microsatellite marker of CA repeats. Genomic DNA was obtained from the peripheral leukocytes of healthy normotensive subjects (NT; 179 men and 100 women, 57±6 years) aging 50 years or more and patients with essential hypertension (EH; 162 men and 98 women, 53±11 years) who had developed hypertension before the age of 50 years. The genomic DNA was subject to PCR using a fluorescence-labeled primer, and the number of CA repeats were determined by poly-acrylamide gel electrophoresis. Plasma AM concentration was measured by RIA and compared with respect to the number of CA repeats adjacent to the AM gene. Results: The averaged blood pressure was 117±13/73±9 mmHg in NT and 170±23/104±12 mmHg in EH when the patients were not treated. In Japanese, there existed four types of allelles with different CA-repeat number; 11, 13, 14 and 19. The frequencies of these alleles were 11: 28.7%, 13: 33.6%, 14: 34.7% and 19: 3.0% in NT and 11: 30.5%, 13: 28.4%, 14:34.3% and 19: 6.8% in EH. Thus, the frequency of 19 CA repeat allele was higher in EH than in NT (χ 2 =10.25, p<0.02). Namely, 13.5% of EH carried the 19-repeat allele, while the frequency was 6.1% in NT (χ 2 =8.43, p<0.004). In NT, plasma concentrations of AM in 21 homozygotes of 11-repeat allele, 27 homozygotes of 13-repeat allele, 30 homozygotes of 14-repeat allele and 17 heterozygotes carrying 19-repeat allele were 7.5±1.0, 7.0±1.3, 7.2±1.3 and 7.3±1.7 fmol/ml, respectively, and the values were not significantly different between the genotypes. Conclusion: Microsatellite DNA polymorphism of AM gene may be associated with the genetic predisposition to EH, although the gene expression is not likely to be affected by the genotypes.
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Murray, A. W., T. E. Claus, and J. W. Szostak. "Characterization of two telomeric DNA processing reactions in Saccharomyces cerevisiae." Molecular and Cellular Biology 8, no. 11 (November 1988): 4642–50. http://dx.doi.org/10.1128/mcb.8.11.4642-4650.1988.
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We have investigated two reactions that occur on telomeric sequences introduced into Saccharomyces cerevisiae cells by transformation. The elongation reaction added repeats of the yeast telomeric sequence C1-3A to telomeric sequences at the end of linear DNA molecules. The reaction worked on the Tetrahymena telomeric sequence C4A2 and also on the simple repeat CA. The reaction was orientation specific: it occurred only when the GT-rich strand ran 5' to 3' towards the end of the molecule. Telomere elongation occurred by non-template-directed DNA synthesis rather than any type of recombination with chromosomal telomeres, because C1-3A repeats could be added to unrelated DNA sequences between the CA-rich repeats and the terminus of the transforming DNA. The elongation reaction was very efficient, and we believe that it was responsible for maintaining an average telomere length despite incomplete replication by template-directed DNA polymerase. The resolution reaction processed a head-to-head inverted repeat of telomeric sequences into two new telomeres at a frequency of 10(-2) per cell division.
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Murray, A. W., T. E. Claus, and J. W. Szostak. "Characterization of two telomeric DNA processing reactions in Saccharomyces cerevisiae." Molecular and Cellular Biology 8, no. 11 (November 1988): 4642–50. http://dx.doi.org/10.1128/mcb.8.11.4642.
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We have investigated two reactions that occur on telomeric sequences introduced into Saccharomyces cerevisiae cells by transformation. The elongation reaction added repeats of the yeast telomeric sequence C1-3A to telomeric sequences at the end of linear DNA molecules. The reaction worked on the Tetrahymena telomeric sequence C4A2 and also on the simple repeat CA. The reaction was orientation specific: it occurred only when the GT-rich strand ran 5' to 3' towards the end of the molecule. Telomere elongation occurred by non-template-directed DNA synthesis rather than any type of recombination with chromosomal telomeres, because C1-3A repeats could be added to unrelated DNA sequences between the CA-rich repeats and the terminus of the transforming DNA. The elongation reaction was very efficient, and we believe that it was responsible for maintaining an average telomere length despite incomplete replication by template-directed DNA polymerase. The resolution reaction processed a head-to-head inverted repeat of telomeric sequences into two new telomeres at a frequency of 10(-2) per cell division.
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Ibrahim, Abdulkhaleg, Christophe Papin, Kareem Mohideen-Abdul, Stéphanie Le Gras, Isabelle Stoll, Christian Bronner, Stefan Dimitrov, Bruno P. Klaholz, and Ali Hamiche. "MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion." Science 372, no. 6549 (June 24, 2021): eabd5581. http://dx.doi.org/10.1126/science.abd5581.
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The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.
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Akkaya, M. S., A. A. Bhagwat, and P. B. Cregan. "Length polymorphisms of simple sequence repeat DNA in soybean." Genetics 132, no. 4 (December 1, 1992): 1131–39. http://dx.doi.org/10.1093/genetics/132.4.1131.
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Abstract The objective of this work was to ascertain the presence and degree of simple sequence repeat (SSR) DNA length polymorphism in the soybean [Glycine max (L.) Merr.]. A search of GenBank revealed no (CA)n or (GT)n SSRs with n greater than 8 in soybean. In contrast, 5 (AT)n and 1 (ATT)n SSRs with n ranging from 14 to 27 were detected. Polymerase chain reaction (PCR) primers to regions flanking the six SSR loci were used in PCR amplification of DNA from 43 homozygous soybean genotypes. At three loci, amplification produced one PCR product per genotype and revealed 6, 7 and 8 product length variants (alleles) at the three loci, respectively. F1 hybrids between parents carrying different alleles produced two PCR products identical to the two parents. Codominant segregation of alleles among F2 progeny was demonstrated at each locus. A soybean DNA library was screened for the presence of (CA/GT)n SSRs. Sequencing of positive clones revealed that the longest such SSR was (CA)9. Thus, (CA)n SSRs with n of 15 or more are apparently much less common in soybean than in the human genome. In contrast to humans, (CA)n SSRs will probably not provide an abundant source of genetic markers in soybean. However, the apparent abundance of long (AT)n sequences should allow this SSR to serve as a source of highly polymorphic genetic markers in soybean.
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Kudryavtseva, E. V., V. V. Kovalev, I. I. Baranov, I. V. Kanivets, Yu K. Kievskaya, and S. A. Korostelev. "Low Fetal Fraction of Cell-free DNA Identified by Non-invasive Prenatal DNA Testing: Possible Causes, Clinical Significance, and Tactics." Doctor.Ru 19, no. 8 (2020): 49–54. http://dx.doi.org/10.31550/1727-2378-2020-19-8-49-54.
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Study Objective: To compare the rates of fetal chromosomal abnormalities (CA) detected during initial non-invasive prenatal DNA testing (NIPT) with the rates of CA found through repeat NIPT in patients with low fetal fraction or low quality of cell-free embryonic DNA. Study Design: This was a retrospective cohort study. Materials and Methods: Twenty-one thousand forty-two women who underwent NIPT in Russia between 2013 and 2018 were included in the study. The main group comprised 1,025 of the 1,044 patients with uninformative results (low fetal fraction result, making it impossible to assess the risk of CA), who consented to repeat NIPT. The control group was made up of 19,998 women who had informative results of initial NIPT. The exclusion group comprised women with low fetal fraction who declined repeat screening. The study method was targeted NIPT. Blood samples were taken from a vein and centrifuged to obtain plasma. Fetal cell-free DNA was analyzed by next-generation sequencing (NGS), a method patented by Natera for sequencing single nucleotide polymorphisms. Study Results: Initial NIPT was uninformative in 1,044 (5%) of the patients and repeat procedure yielded informative results in 821 (80.1%) out of 1,025 patients. Among the patients with informative results from the initial study, the rate of chromosomal aneuploidies was 2.4%. In the group of women with informative results from the repeat procedure, fetal CA were detected in 27 (3.3%) cases. In the subgroup of women with informative results only after a third NIPT, the prevalence of CA was 9.3% (seven out of 75 cases). The study showed that in women carrying fetuses with trisomy 18 or 13 or monosomy X, mean fetal fraction in the first trimester was significantly lower than normal. In the second trimester, significantly lower than normal fetal fraction was observed in women carrying fetuses with trisomy 18 or monosomy X. There was a statistically significant difference in fetal fraction levels between patients with body weight <50 kg and those with body weight 80-89 kg or above (р<0.05). Conclusion: The probability of detecting CA by repeat NIPT is significantly higher than in an initial procedure. If initial testing is not informative, it should be repeated. If the second procedure also fails to yield informative results, invasive prenatal diagnosis should be considered. Fetal fraction levels are lower in heavier women. Thus, other methods of prenatal diagnosis should be recommended for overweight and obese women. Keywords: non-invasive prenatal DNA testing, fetal fraction, prenatal diagnosis, Down syndrome.
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Peng, Xu, Kim Brügger, Biao Shen, Lanming Chen, Qunxin She, and Roger A. Garrett. "Genus-Specific Protein Binding to the Large Clusters of DNA Repeats (Short Regularly Spaced Repeats) Present in Sulfolobus Genomes." Journal of Bacteriology 185, no. 8 (April 15, 2003): 2410–17. http://dx.doi.org/10.1128/jb.185.8.2410-2417.2003.
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ABSTRACT Short regularly spaced repeats (SRSRs) occur in multiple large clusters in archaeal chromosomes and as smaller clusters in some archaeal conjugative plasmids and bacterial chromosomes. The sequence, size, and spacing of the repeats are generally constant within a cluster but vary between clusters. For the crenarchaeon Sulfolobus solfataricus P2, the repeats in the genome fall mainly into two closely related sequence families that are arranged in seven clusters containing a total of 441 repeats which constitute ca. 1% of the genome. The Sulfolobus conjugative plasmid pNOB8 contains a small cluster of six repeats that are identical in sequence to one of the repeat variants in the S. solfataricus chromosome. Repeats from the pNOB8 cluster were amplified and tested for protein binding with cell extracts from S. solfataricus. A 17.5-kDa SRSR-binding protein was purified from the cell extracts and sequenced. The protein is N terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also recognizes both main families of repeat sequences in S. solfataricus. The recombinant protein, expressed in Escherichia coli, showed the same binding properties to the SRSR repeat as the native one. The SSO454 protein exhibits a tripartite internal repeat structure which yields a good sequence match with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure at the center of each DNA repeat and thereby produces a binding site for another protein, possibly a more conserved one, in a process that may be essential for higher-order stucturing of the SRSR clusters.
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Sullivan, Alexis R., Yrin Eldfjell, Bastian Schiffthaler, Nicolas Delhomme, Torben Asp, Kim H. Hebelstrup, Olivier Keech, et al. "The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants." Genome Biology and Evolution 12, no. 1 (November 27, 2019): 3586–98. http://dx.doi.org/10.1093/gbe/evz263.
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Abstract Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.
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Korom, E., K. Bakos, G. Veress, O. Pinke, K. M. Reed, L. Varga, and B. Kovács. "Isolation of 11 new polymorphic microsatellites from CA enriched turkey genomic libraries (Short communication)." Archives Animal Breeding 53, no. 5 (October 10, 2010): 618–22. http://dx.doi.org/10.5194/aab-53-618-2010.
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Abstract. Microsatellite loci from the ancient Hungarian variety of the Broad Breasted Bronze Turkey (Meleagris gallopavo) were isolated. CA-repeat enriched libraries were constructed from DNA of randomly collected samples. Libraries were screened for repeat-containing clones by PIMA (PCR Isolation of Microsatellite Arrays) and the DNA-sequence of 167 positive clones was determined. A total of 136 microsatellite repeat-containing sequences were found, 59 sequences were unique. Comparing these with the genomic databases, we found 7 previously annotated microsatellite sequences. The newly isolated 52 microsatellites were tested on the mapping population of the University of Minnesota, and the map position of 11 microsatellites was determined.
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Wang, J., S. Zhang, and R. Lai. "Epidermal growth factor receptor intron 1 (CA)n dinucleotide repeat polymorphism and mutations associated with the responsiveness of molecular targeted therapy in lung cancer." Journal of Clinical Oncology 27, no. 15_suppl (May 20, 2009): e14595-e14595. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.e14595.
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e14595 Background: To explore EGFR gene intron 1 (CA)n repeat polymorphism and mutations associated with the responsiveness of molecular targeted therapy in lung cancer. Methods: Both observed groups consisted of 116 somatic specimens of lung cancer and controls consisted of 20 peripheral blood samples were analyzed by direct DNA sequencing of EGFR mutations at exons 18,19,21. Also (CA)n repeat polymorphisms in intron 1 of EGFR from 48 specimens were analyzed. 45 lung cancer patients were followed up. Results: EGFR mutations were found in 24 of 116 somatic specimens (20.69%). Response rate and disease control rate to EGFR TKIs was significantly higher in the patients with EGFR mutations (62.5% vs. 0)(P<0.0l),(100% vs.44.4%) (P<0.05)respectively than those without it in observed groups.In patients harboring EGFR mutations, disease control rate to patients treated with Iressa (100%) was significantly higher than those who never treated with it (40%)(P<0.05). The frequency distribution of EGFR intron 1 (CA)n repeat in 48 specimens was 23(47.9%)low (CA)n repeat(CA≤16)and 25 (52.1%) high repeat(CA>16). There was no significant difference in response rate and disease control rate of EGFR TKIs treatment between low and high (CA)n repeat numbers both in 16 patients with mutations and 18 patients without mutations in observed groups(P>0.05). Conclusions: Somatic mutations of EGFR is a major determinant of EGFR TKIs response in lung cancer. There was no significant difference in response rate and disease control rate of EGFR TKIs treatment between low (CA) n repeat patients and high repeat ones under the consideration of the mutant factor. No significant financial relationships to disclose.
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Garcia-Donas, J., S. Leskelä, J. M. Sanchez, J. C. Camara, N. Rodriguez, P. Dhimes, F. Pinedo, J. L. Lopez, C. Jara, and C. Rodriguez-Antona. "Correlation between the EGFR intron 1 CA dinucleotide repeat and skin toxicity in lung cancer patients treated with erlotinib." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 14001. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.14001.
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14001 Background: Acneiform rash is the main toxicity of erlotinib, an epidermal growth factor receptor (EGFR) inhibitor. The length of the CA dinucleotide repeat in EGFR intron 1 has been suggested to predict the biological effects of tyrosin kinase inhibitors. Thus, we compared this polymorphism with the rash severity in non-small cell lung cancer (NSCLC) patients treated with erlotinib. Methods: Toxicity was evaluated in 18 metastatic or locally advanced unresectable NSCLC patients treated orally with 150 mg/d of erlotinib: 7 retrospectively and 11 prospectively. Rash was graded according to a modified scale based on the Common Toxicity Criteria v.3.0, which subclassified grade II rash into IIA (topic intervention indicated) and IIB (oral intervention indicated). Genomic DNA was isolated from each patient; the length of the EGFR intron 1 CA dinucleotide repeat was measured by PCR amplification and analyzed on a capillary sequencer. Results: The most common EGFR genotypes were: 16, 20, 17 and 18 CA repeats (with 50, 25, 8 and 8% frequency, respectively). 33% of the subjects with a total amount of CA repeats <34 had grade IIB-III rash vs 11% of the subjects with =34 CA repeats. In addition, all patients with 0 grade toxicity belonged to the =34 CA group. When the only patient with a previous dermatological disease (psoriasis) was excluded from the analysis, the difference between both groups increased, reaching statistical significance (p=0.047). Conclusions: This data suggests that NSCLC patients with long EGFR intron 1 CA alleles present lower grades of skin toxicity when treated with erlotinib than patients with short CA alleles. Further studies are required to confirm this data. [Table: see text] No significant financial relationships to disclose.
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Khasa, P. D., C. H. Newton, M. H. Rahman, B. Jaquish, and B. P. Dancik. "Isolation, characterizaton, and inheritance of microsatellite loci in alpine larch and western larch." Genome 43, no. 3 (June 1, 2000): 439–48. http://dx.doi.org/10.1139/g99-131.
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Microsatellite loci or simple sequence repeat loci (SSRs) were isolated in alpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.). In total, 14 SSR loci were characterized; two [(TCT)4, A7] came from published Larix DNA sequence data, one (CA)17 was obtained from a partial non-enriched alpine larch total genomic DNA library, and the remaining 11 loci were obtained from larch genomic DNAs enriched for (CA)n repeats. The SSR regions in these clones could be divided into three categories: perfect repeat sequences without interruption, imperfect repeat sequences with interruption(s), and compound repeat sequences with adjacent tandem simple dinucleotides. Eight of the 14 loci analyzed were found to be polymorphic and useful markers after silver-staining polyacrylamide gel electrophoresis. In addition, several SSR primers developed for alpine larch were able to successfully amplify polymorphic loci in its related species, western larch, and among other closely related taxa within the Larix genus. The inheritance of microsatellite loci was verified by analysis of haploid megagametophyte and diploid embryo tissues of progeny obtained from controlled crosses between western larch and alpine larch. All microsatellite loci analyzed had alleles that segregated according to expected Mendelian frequencies. Two species-specific markers (UAKLly10a and UAKLla1) allow easy and rapid identification of specific genetic entry of alpine larch and western larch at any stage in the sporophyte phase of the life cycle. Therefore, these markers are efficient in identifying the parental species and to validate controlled crosses between these two closely related species. These results are important in tree improvement programs of alpine larch and western larch aimed at producing genetically improved hybrid stock for reforestation in Western Canada and U.S.A.Key words: database search, enriched library, inheritance, Larix, microsatellites, simple sequence repeats, PCR.
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Yuxiang, Wang, T. E. Peretolchina, E. V. Romanova, and D. Y. Sherbakov. "Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal." Vavilov Journal of Genetics and Breeding 27, no. 4 (July 14, 2023): 349–56. http://dx.doi.org/10.18699/vjgb-23-42.
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DNA repeat composition of low coverage (0.1–0.5) genomic libraries of four amphipods species endemic to Lake Baikal (East Siberia) and four endemic gastropod species of the fam. Baicaliidae have been compared to each other. In order to do so, a neighbor joining tree was inferred for each quartet of species (amphipods and mollusks) based on the ratio of repeat classes shared in each pair of species. The topology of this tree was compared to the phylogenies inferred for the same species from the concatenated protein-coding mitochondrial nucleotide sequences. In all species analyzed, the fraction of DNA repeats involved circa half of the genome. In relatively more ancient amphipods (most recent common ancestor, MRCA, existed approximately sixty millions years ago), the most abundant were species-specific repeats, while in much younger Baicaliidae (MRCA equal to ca. three millions years) most of the DNA repeats were shared among all four species. If the presence/absence of a repeat is regarded as a separate independent trait, and the ratio of shared to total numbers of repeats in a species pair is used as the measure of distance, the topology of the NJ tree is the same as the quartet phylogeny inferred for the mitogenomes protein coding nucleotide sequences. Meanwhile, in each group of species, a substantial number of repeats were detected pointing to the possibility of non-neutral evolution or a horizontal transfer between species occupying the same biotope. These repeats were shared by non-sister groups while being absent in the sister genomes. On the other hand, in such cases some traits of ecological significance were also shared.
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ISHIBASHI, Yasuyuki, Syuiti ABE, and Michihiro C. YOSHIDA. "DNA fingerprinting of animal genomes by CA-repeat primed polymerase chain reaction." Genes & Genetic Systems 70, no. 1 (1995): 75–78. http://dx.doi.org/10.1266/ggs.70.75.
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ISHIBASHI, Yasuyuki, Syuiti ABE, and Michihiro C. YOSHIDA. "DNA fingerprinting of animal genomes by CA-repeat primed polymerase chain reaction." Japanese Journal of Genetics 70, no. 1 (1995): 75–78. http://dx.doi.org/10.1266/jjg.70.75.
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Gardiner, J. M., S. Chao, and E. H. Coe. "Cloning maize telomeres by complementation in Saccharomyces cerevisiae." Genome 39, no. 4 (August 1, 1996): 736–48. http://dx.doi.org/10.1139/g96-093.
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Maize telomeric restriction fragments were cloned by virtue of their ability to function as telomeres on a linear plasmid in Saccharomyces cerevisiae. Nine maize telomeric YAC transformants (MTYs) were selected by hybridization to the Arabidopsis telomere repeat (CCCTAAA) from a pool of 1537 primary transformants. Bal31 digestion of MTY3 and MTY9 DNA indicated that the telomere hybridizing tracts are located at the terminus of the linear chromosome and therefore function as telomeres in yeast. Subclones generated for pMTY7 (pMTY7SC1) and pMTY9 (pMTY9ER) hybridized to Bal31 sensitive restriction fragments in maize DNA, indicating that maize telomeric restriction fragments had been cloned. Both pMTY7SC and pMTY9ER detected telomeric RFLPs, allowing the endpoints of seven chromosome arms to be determined. Additionally, pMTY7ER mapped to the centromeric regions of chromosomes 2 and 3, suggesting a relationship between centromeric and telomeric sequences. DNA sequencing of pMTY7SC and pMTY9ER revealed that both subclones contained CA-rich regions with sporadic occurrences of the telomere repeat and its degenerate repeats. Key words : maize, telomere, RFLP, telomeric.
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Ahmad, Riaz, Louise Ferguson, and Stephen M. Southwick. "Identification of Pistachio (Pistacia vera L.) Nuts with Microsatellite Markers." Journal of the American Society for Horticultural Science 128, no. 6 (November 2003): 898–903. http://dx.doi.org/10.21273/jashs.128.6.0898.
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A genomic DNA library enriched for dinucleotide (CT)n and (CA)n and trinucleotide (CTT)n microsatellite motifs has been developed from `Kerman' pistachio (Pistacia vera L.). The enrichment method based on magnetic or biotin capture of repetitive sequences from restricted genomic DNA revealed an abundance of simple sequence repeats (SSRs) in the pistachio genome which were used for marker development. After an enrichment protocol, about 64% of the clones contained (CT)n repeats while 59% contained (CA)n for CT and CA enriched libraries, respectively. In the (CT)n enriched library, compound sequences were 45% while for (CA)n it was 13.5%. In both dinucleotide enriched libraries, about 80% of the clones having microsatellites have a repeat length in the range of 10 to 30 units. A library enriched for trinucleotide (CTT)n contained <19% of the clones with (CTT)n repeats. Of the clones that contained microsatellites, 62% had sufficient flanking sequence for primer design. An initial set of 25 pairs of primers was designed, out of which 14 pairs amplified cleanly and produced an easily interpretable PCR product in the commercially important American, Iranian, Turkish, and Syrian pistachio cultivars. The efficient DNA extraction method developed for pistachio kernels and shells (roasted and nonroasted) yielded DNA of sufficient quality to use PCR to create DNA fingerprints. In total, 46 alleles were identified by 14 primer pairs and a dendrogram was constructed on the basis of that information. The SSR markers distinguished most of the tested cultivars from their unique DNA fingerprint. An UPGMA cluster analysis placed most of the Iranian samples in one group while the Syrian samples were the most diverse and did not constitute a single distinct group. The maximum number of cultivar specific markers were found in `Kerman'(4), the current industry standard in the United States, and the Syrian cultivar Jalab (5). The technique of using extracted DNA from pistachio kernal or shell coupled with the appropriate marker system developed here, can be used for analyses and measurement of trueness to type.
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Hirai, K., K. Irifune, R. Tanaka, and H. Morikawa. "Molecular and cytological characterization of a highly repeated DNA sequence in Raphanus sativus." Genome 38, no. 6 (December 1, 1995): 1237–43. http://dx.doi.org/10.1139/g95-162.
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A highly repeated DNA sequence with a repeat unit of ca. 180 bp was found in genomic DNA HindIII-digests of Raphanus sativus. The repeating units of six isolated, independent clones were sequenced. These units have 177 or 178 bp, are 36% G+C in their DNA base composition, and show 90% sequence homology. The copy number of this 180-bp repeat unit is about 0.5 × 106 per diploid genome. In situ hybridization analysis with the repeating unit as the probe and C-banding analysis indicated that the repeated DNA sequence of R. sativus is closely associated with the major C-heterochromatins in the proximal regions of all 18 chromosomes at mitotic metaphase.Key words: Raphanus sativus, repeated DNA sequence, nucleotide sequence, in situ hybridization, C-banding.
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Pucci, Marcela B., Patricia Barbosa, Viviane Nogaroto, Mara C. Almeida, Roberto F. Artoni, Priscila C. Scacchetti, José C. Pansonato-Alves, Fausto Foresti, Orlando Moreira-Filho, and Marcelo R. Vicari. "Chromosomal Spreading of Microsatellites and (TTAGGG)n Sequences in the Characidium zebra and C. gomesi Genomes (Characiformes: Crenuchidae)." Cytogenetic and Genome Research 149, no. 3 (2016): 182–90. http://dx.doi.org/10.1159/000447959.
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Sex chromosome evolution involves the accumulation of repeat sequences such as multigenic families, noncoding repetitive DNA (satellite, minisatellite, and microsatellite), and mobile elements such as transposons and retrotransposons. Most species of Characidium exhibit heteromorphic ZZ/ZW sex chromosomes; the W is characterized by an intense accumulation of repetitive DNA including dispersed satellite DNA sequences and transposable elements. The aim of this study was to analyze the distribution pattern of 18 different tandem repeats, including (GATA)n and (TTAGGG)n, in the genomes of C. zebra and C. gomesi, especially in the C. gomesi W chromosome. In the C. gomesi W chromosome, weak signals were seen for (CAA)10, (CAC)10, (CAT)10, (CGG)10, (GAC)10, and (CA)15 probes. (GA)15 and (TA)15 hybridized to the autosomes but not to the W chromosome. The (GATA)n probe hybridized to the short arms of the W chromosome as well as the (CG)15 probe. The (GATA)n repeat is known to be a protein-binding motif. GATA-binding proteins are necessary for the decondensation of heterochromatic regions that hold coding genes, especially in some heteromorphic sex chromosomes that may keep genes related to oocyte development. The (TAA)10 repeat is accumulated in the entire W chromosome, and this microsatellite accumulation is probably involved in the sex chromosome differentiation process and crossover suppression in C. gomesi. These additional data on the W chromosome DNA composition help to explain the evolution of sex chromosomes in Characidium.
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Smith, David N., and Michael E. Devey. "Occurrence and inheritance of microsatellites in Pinus radiata." Genome 37, no. 6 (December 1, 1994): 977–83. http://dx.doi.org/10.1139/g94-138.
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Microsatellites are an important class of DNA marker because of their abundance and length hypervariability. As part of a project mapping the Pinus radiata genome, we have characterized some of the microsatellites in this species. Southern blots were screened with oligonucleotide probes [(CA)10, (GA)10, (GAA)9, (CAA)8, (CAC)5, (GACA)4] to assess their abundance. CA and GA were the most abundant microsatellites, while GAA was least abundant. A genomic library in lambda ZAP, covering 9 × 104 kb, was screened with a combined poly(CA) + poly(GA) probe and yielded 120 positives, approximately one CA or GA microsatellite every 750 kb of the P. radiata genome. It was found that 25% of the positives were embedded within highly repetitive DNA. Four of the five subclones sequenced contained compound microsatellites, with TA predominating as the additional repeat. Segregation analysis of PCR products for two microsatellites, PR4.6 and PR9.3, in 96 progeny of a controlled out-cross verified simple Mendelian inheritance. Both loci are highly polymorphic with Polymorphism Information Content values of 0.63 and 0.70 for PR4.6 and PR9.3, respectively. These results indicate that microsatellites are abundant in a conifer genome and can be valuable markers for pine mapping, fingerprinting, and population genetic studies.Key words: microsatellites, dinucleotide repeats, conifer genome, sequence tagged sites.
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Jensen, Julia R., and Ryan B. Jensen. "Abstract 5603: Defining the functions of the BRCA2 BRC repeats in modulating RAD51 binding and activity." Cancer Research 84, no. 6_Supplement (March 22, 2024): 5603. http://dx.doi.org/10.1158/1538-7445.am2024-5603.
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Abstract The BRCA2 (Breast Cancer Susceptibility 2) gene is critical for preserving genome integrity by regulating homology-directed repair (HDR) of DNA double-strand breaks (DSBs). Germline mutations in BRCA2 predispose individuals to a high risk for ovarian, breast, prostate, and pancreatic cancer. BRCA2 contains eight BRC repeats that mediate binding to RAD51. It remains unclear how exactly the different BRC repeats regulate RAD51 functions. In our study, we explore the importance of each BRC repeat, their interconnections, and their impact on RAD51 binding and filament stability. We engineered amino acid substitutions into the BRC FxTAS motif required for specific contacts within a hydrophobic binding pocket of RAD51 to disrupt BRC binding to RAD51. We further created mutations in RAD51 (F86E/A89E) that either prevent self-association but retain binding to the BRC repeats or a mutation (K133R) that results in a hyper-stable RAD51 nucleoprotein filament. Using both cell-based models and biochemical analyses, we have begun studies to parse out the specific functions of each BRC repeat. Our ultimate goal is to incorporate single amino acid changes into each BRC repeat within the context of the full-length BRCA2 protein to comprehensively characterize the contribution of each BRC repeat to HDR and response to chemotherapeutics such as PARP inhibitors. Citation Format: Julia R. Jensen, Ryan B. Jensen. Defining the functions of the BRCA2 BRC repeats in modulating RAD51 binding and activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5603.
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Srinivasan, Rajini, Nataliya Nady, Neha Arora, Laura J. Hsieh, Tomek Swigut, Geeta J. Narlikar, Mark Wossidlo, and Joanna Wysocka. "Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage." Science Advances 6, no. 12 (March 2020): eaaz9115. http://dx.doi.org/10.1126/sciadv.aaz9115.
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Zinc finger protein Zscan4 is selectively expressed in mouse two-cell (2C) embryos undergoing zygotic genome activation (ZGA) and in a rare subpopulation of embryonic stem cells with 2C-like features. Here, we show that Zscan4 specifically recognizes a subset of (CA)n microsatellites, repeat sequences prone to genomic instability. Zscan4-associated microsatellite regions are characterized by low nuclease sensitivity and high histone occupancy. In vitro, Zscan4 binds nucleosomes and protects them from disassembly upon torsional strain. Furthermore, Zscan4 depletion leads to elevated DNA damage in 2C mouse embryos in a transcription-dependent manner. Together, our results identify Zscan4 as a DNA sequence–dependent microsatellite binding factor and suggest a developmentally regulated mechanism, which protects fragile genomic regions from DNA damage at a time of embryogenesis associated with high transcriptional burden and genomic stress.
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Wyngaard, G. A., I. A. McLaren, M. M. White, and J. M. Sévigny. "Unusually high numbers of ribosomal RNA genes in copepods (Arthropoda: Crustacea) and their relationship to genome size." Genome 38, no. 1 (February 1, 1995): 97–104. http://dx.doi.org/10.1139/g95-012.
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We report on copy numbers of 18S ribosomal RNA genes in three species of copepods (Crustacea: Copepoda), two of which possess an unusual arrangement in which 5S genes are included within the 18S–5.8S–28S repeat unit. Slot blots of genomic and standard DNA were hybridized with an 18S rRNA gene probe constructed from one of the marine species and hybridization was quantified using chemiluminescence. Diploid 18S rRNA gene copy numbers are estimated as ca. 15 300 and 33 500 in the marine species Calanus finmarchicus (13.0 pg DNA in 2C adult nuclei) and C. glacialis (24.2 pg DNA), respectively, and ca. 840 and 730 in two freshwater populations of Mesocyclops edax (both ca. 3 pg DNA) from Virginia and Nova Scotia, respectively. The roughly proportional relationship between 2C somatic nuclear DNA contents and rRNA gene copy number in the sibling species C. finmarchicus and C. glacialis may reflect polytenic replication of entire genomes during abrupt speciation events. Copy numbers may also reflect differential losses during embryonic chromatin diminution.Key words: rRNA genes, copy number, genome size, Calanus, Mesocyclops.
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Iqbal, M. J., L. J. Grauke, A. S. Reddy, and T. E. Thompson. "066 Development of Simple Sequence Repeat DNA Markers for Use in Pecan Genetic Studies." HortScience 34, no. 3 (June 1999): 452D—452. http://dx.doi.org/10.21273/hortsci.34.3.452d.
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A microsatellite library has been developed from `Halbert', a native pecan selection from Coleman County, Texas, using methods developed at the Texas A&M Univ. Crop Biotechnology Center. A total of 6144 DNA fragment clones were archived in 384 well plates for screening. Four-hundred-thirty-nine clones were positive after Southern hybridization using di- and tri-nucleotide repeats as probes. One-hundred-twenty-five positive clones were sequenced on an ABI 377 automated DNA sequencer. Of these, 24 repeats had enough sequences at the two ends to design primers. Primers were designed using Primer Express software, and were synthesized by Genosys, USA. The simple sequence repeats (SSRs) chosen for primer analysis include di- (CA and GA) and tri-nucleotide repeats (CTT, GAA and GAT). The SSRs were amplified under high stringency conditions with temperatures based on length and GC content. Reproducibility was verified using `Halbert' DNA isolated from different inventories. Of the 24 primer pairs tested, 20 successfully amplified microsatellites from `Halbert'. DNA was isolated from 48 pecan and hickory accessions selected to strategically represent the genetic diversity of the NCGR Carya collections (a core collection). The accessions included parent-progeny combinations, individuals from geographically distant native populations, species, and interspecific hybrids. The 20 SSR primers that produced good amplification products in `Halbert' were used to evaluate the collection, with 11 revealing multiple sizes of the repeat. The number of bands amplified with different primer combinations ranged from 4 to 32 in the 48 genotypes tested. We used RFLPscan software to aid in gel scoring (sizing amplified fragments, and comparing amplification profiles), and NTSYSpc software to evaluate genetic similarities. Evaluation of the data confirms the utility of the primers in delimiting known relationships.
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Annapragada, Akshaya, Noushin Niknafs, James R. White, Daniel C. Bruhm, Christopher Cherry, Jamie E. Medina, Vilmos Adleff, et al. "Abstract 988: Genome-wide repeat landscapes in cancer and cell-free DNA." Cancer Research 84, no. 6_Supplement (March 22, 2024): 988. http://dx.doi.org/10.1158/1538-7445.am2024-988.
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Abstract Introduction: Repeat sequences comprise >50% of the human genome and structural and epigenetic changes in these regions are implicated in cancer. However, no systematic analysis of the compendium of repeat sequences has ever been performed in human cancer or cell-free DNA (cfDNA), largely due to the inability to identify and quantify repeat sequences genome-wide. We describe here the first comprehensive analysis of genome-wide repeat landscapes in cancer and demonstrate their utility in cfDNA liquid biopsies. Methods: We developed ARTEMIS (Analysis of RepeaT EleMents in dISease) an alignment-free, genome-wide approach for analyzing repeat landscapes in short read sequencing. This approach uses a de novo search of short sequences (kmers) in the telomere to telomere (chm13) reference genome to identify 1.2 billion 24-mers uniquely defining 1280 individual repeat types occurring genome-wide across 57 subfamilies and 6 families. We analyzed ARTEMIS kmers in whole genome sequences of 525 matched tumor/normal pairs from breast, colorectal, liver, lung, ovarian, cervical, prostate, thyroid, head and neck, gastric, and bladder cancers in the Pan Cancer Analysis of Whole Genomes (PCAWG), and in low coverage (1-2x) whole genome sequences of 1450 cfDNA samples from individuals with and without 8 types of cancer. Results: Analysis of ARTEMIS kmer repeat landscapes in 525 PCAWG tumors identified changes in all 1280 repeat element types, including 820 novel elements not previously known to be altered in cancer. A median of 807 repeat elements (range 246-1280) were altered in each tumor compared to its matched normal. The majority of changes were in repeat elements not previously described as altered in tumorigenesis and were most frequently found within Satellites, LINEs and SINEs, though changes were also observed in LTRs, Transposable Elements, and RNA Elements. A cross-validated cfDNA model using repeat landscapes (ARTEMIS) and fragmentation features (DELFI) detected individuals in a diagnostic cohort (n=287) across all stages of lung cancer with high performance (AUC 0.91, 95% CI 0.88-0.95) and was externally validated in a separate population (n=513). The locked model generated scores that correlated with circulating tumor mutant allele fractions for patients (n=19) undergoing targeted lung cancer therapy (r=0.80, p<2.2e-16), and stratified progression-free survival (p<0.001). ARTEMIS repeat landscape analyses of cfDNA also detected liver cancer in a high-risk cohort (n=208) of individuals with cirrhosis or viral hepatitis (AUC 0.91, 95% CI 0.87-0.95), and identified tissue of origin among seven tumor types (n=423). Conclusions: ARTEMIS reveals genome-wide repeat landscapes in human cancer, including in 820 novel elements not previously known to be altered in tumorigenesis. These repeat landscapes that can now be described are evaluable in the circulation and provide an avenue for noninvasive detection and characterization of cancer. Citation Format: Akshaya Annapragada, Noushin Niknafs, James R. White, Daniel C. Bruhm, Christopher Cherry, Jamie E. Medina, Vilmos Adleff, Carolyn Hruban, Dimitrios Mathios, Zachariah H. Foda, Jillian Phallen, Robert B. Scharpf, Victor E. Velculescu. Genome-wide repeat landscapes in cancer and cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 988.
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Yu, Ju-Kyung, Jodie Mangor, Lucy Thompson, Keith J. Edwards, Mary B. Slabaugh, and Steven J. Knapp. "Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower." Genome 45, no. 4 (August 1, 2002): 652–60. http://dx.doi.org/10.1139/g02-025.
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Simple sequence repeat (SSR) markers were developed for cultivated sunflower (Helianthus annuus L.) from the DNA sequences of 970 clones isolated from genomic DNA libraries enriched for (CA)n, (CT)n, (CAA)n, (CATA)n, or (GATA)n. The clones harbored 632 SSRs, of which 259 were unique. SSR markers were developed for 130 unique SSRs by designing and testing primers for 171 unique SSRs. Of the total, 74 SSR markers were polymorphic when screened for length polymorphisms among 16 elite inbred lines. The mean number of alleles per locus was 3.7 for dinucleotide, 3.6 for trinucleotide, and 9.5 for tetranucleotide repeats and the mean polymorphic information content (PIC) scores were 0.53 for dinucleotide, 0.53 for trinucleotide, and 0.83 for tetranucleotide repeats. Cluster analyses uncovered patterns of genetic diversity concordant with patterns produced by RFLP fingerprinting. SSRs were found to be slightly more polymorphic than RFLPs. Several individual SSRs were significantly more polymorphic than RFLP and other DNA markers in sunflower (20% of the polymorphic SSR markers had PIC scores ranging from 0.70 to 0.93). The newly developed SSRs greatly increase the supply of sequence-based DNA markers for DNA fingerprinting, genetic mapping, and molecular breeding in sunflower; however, several hundred additional SSR markers are needed to routinely construct complete genetic maps and saturate the genome.Key words: microsatellites, Helianthus, Compositae, DNA polymorphisms.
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Diwan, Noa, Arvind A. Bhagwat, Gary B. Bauchan, and Perry B. Cregan. "Simple sequence repeat DNA markers in alfalfa and perennial and annual Medicago species." Genome 40, no. 6 (December 1, 1997): 887–95. http://dx.doi.org/10.1139/g97-115.
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Simple sequence repeat (SSR) or microsatellite DNA markers have been shown to function well in plant and mammalian species for genetic map construction and genotype identification. The objectives of the work reported here were to search GenBank for the presence of SSR-containing sequences from the genus Medicago, to assess the presence and frequency of SSR DNA in the alfalfa (Medicago sativa (L.) L. &L.) genome, and to examine the function of selected markers in a spectrum of perennial and annual Medicago species. The screening of an alfalfa genomic DNA library and sequencing of clones putatively containing SSRs indicated approximately 19 000 (AT)n + (CT)n + (CA)n + (ATT)n SSRs in the tetraploid genome. Inheritance was consistent with Mendelian expectations at four selected SSR loci with different core motifs. Additionally, genotypes of a range of Medicago species, including 10 perennial subspecies of the M. sativa complex and other perennial and annual Medicago species, were analyzed at each of the loci to ascertain the presence, number, and size of SSR alleles at each locus in each genotype. These studies indicate that SSR markers can function in alfalfa for the construction of genetic maps and will also be useful in a range of Medicago species for purposes of assessing genetic relatedness and taxonomic relationships, and for genotype identification.Key words: microsatellites, SSR markers, simple sequence repeats, alfalfa, annual medics.
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Zhou, Lijuan, Charles A. Powell, Michele T. Hoffman, Wenbin Li, Guocheng Fan, Bo Liu, Hong Lin, and Yongping Duan. "Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont “Candidatus Liberibacter asiaticus” as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats." Applied and Environmental Microbiology 77, no. 18 (July 22, 2011): 6663–73. http://dx.doi.org/10.1128/aem.05111-11.
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ABSTRACT“CandidatusLiberibacter asiaticus” is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of “Ca. Liberibacter” associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (hyvIandhyvII) were identified in the prophage regions of the Psy62 “Ca.Liberibacter asiaticus” genome. Sequence analyses of thehyvIandhyvIIgenes in 35 “Ca.Liberibacter asiaticus” DNA isolates collected globally revealed that thehyvIgene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, whilehyvIIcontains up to 2 NITRs and 4 partial repeats and shares homology withhyvI. Frequent deletions or insertions of these repeats within thehyvIandhyvIIgenes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of “Ca.Liberibacter asiaticus” bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single “Ca.Liberibacter asiaticus”-infected sample. This is the first evidence of different “Ca.Liberibacter asiaticus” populations coexisting in a single HLB-affected sample. The Florida “Ca.Liberibacter asiaticus” isolates contain bothhyvIandhyvII, while all other global “Ca.Liberibacter asiaticus” isolates contain either one or the other. Interclade assignments of the putative HyvIand HyvIIproteins from Florida isolates with other global isolates in phylogenetic trees imply multiple “Ca.Liberibacter asiaticus” populations in the world and a multisource introduction of the “Ca.Liberibacter asiaticus” bacterium into Florida.
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Kolkenbrock, Stephan, Bianca Naumann, Michael Hippler, and Susanne Fetzner. "A Novel Replicative Enzyme Encoded by the Linear Arthrobacter Plasmid pAL1." Journal of Bacteriology 192, no. 19 (July 30, 2010): 4935–43. http://dx.doi.org/10.1128/jb.00614-10.
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ABSTRACT The soil bacterium Arthrobacter nitroguajacolicus Rü61a contains the linear plasmid pAL1, which codes for the degradation of 2-methylquinoline. Like other linear replicons of actinomycetes, pAL1 is characterized by short terminal inverted-repeat sequences and terminal proteins (TPpAL1) covalently attached to its 5′ ends. TPpAL1, encoded by the pAL1.102 gene, interacts in vivo with the protein encoded by pAL1.101. Bioinformatic analysis of the pAL1.101 protein, which comprises 1,707 amino acids, suggested putative zinc finger and topoisomerase-primase domains and part of a superfamily 2 helicase domain in its N-terminal and central regions, respectively. Sequence motifs characteristic of the polymerization domain of family B DNA polymerases are partially conserved in a C-terminal segment. The purified recombinant protein catalyzed the deoxycytidylation of TPpAL1 in the presence of single-stranded DNA templates comprising the 3′-terminal sequence (5′-GCAGG-3′), which in pAL1 forms the terminal inverted repeat, but also at templates with 5′-(G/T)CA(GG/GC/CG)-3′ ends. Enzyme assays suggested that the protein exhibits DNA topoisomerase, DNA helicase, and DNA- and protein-primed DNA polymerase activities. The pAL1.101 protein, therefore, may act as a replicase of pAL1.
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Gebhardt, F., H. BÜrger, and B. Brandt. "Modulation of EGFR Gene Transcription by a Polymorphic Repetitive Sequence – a Link between Genetics and Epigenetics." International Journal of Biological Markers 15, no. 1 (January 2000): 105–10. http://dx.doi.org/10.1177/172460080001500120.
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The epidermal growth factor receptor (EGFR) plays a crucial role in growth, differentiation and motility of normal as well as tumor cells. The transduction of extracellular signals to the cytoplasm via the receptor not only depends on ligand binding, but is also determined by the receptor density on the cell surface. Therefore, with regard to cancer diagnosis and therapeutic approaches targeting EGFR it is important to know how the expression level of EGFR is controlled. We found that transcription activity declines with increasing numbers of CA dinucleotides of a highly polymorphic CA repeat in the first intron of the epidermal growth factor receptor gene. In vivo data from cultured cell lines support these findings, although other regulation mechanisms can compensate this effect. In addition, we showed that RNA elongation terminates at a site closely downstream of the simple sequence repeat (SSR) and that there are two separate major transcription start sites. Model calculations for the helical DNA conformation revealed a high bendability in the EGFR polymorphic region, especially if the CA stretch is extended. These data suggest that the CA-SSR can act like a joint, bringing the promoter in proximity to a putative repressor protein bound downstream of the CA-SSR. The data indicate that this polymorphism may be a marker for cancer, linking genetic and epigenetic risk factors. Furthermore, in breast cancer, heterozygous tumors with short CA-SSR showed an elevated EGFR-expression in contrast to tumours with longer CA-SSR. Tumours with loss of heterozygosity in intron 1 of egfr revealed an increased EGFR expression if the longer allele was lost. Moreover, decreased EGFR gene levels were significantly correlated with poor prognosis in breast cancer.
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Amer, Sayed Amin, Maha Nawar Alotaibi, Sajjad Shahid, Mahmoud Alsafrani, and Abdul Rauf Chaudhary. "Short Tandem Repeat (STR) Profiling of Earwax DNA Obtained from Healthy Volunteers." Current Issues in Molecular Biology 45, no. 7 (July 10, 2023): 5741–51. http://dx.doi.org/10.3390/cimb45070362.
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The present study aimed to establish human earwax as a potential source of DNA evidence that could be effectively used in human identification. Sixty earwax samples were obtained from 15 healthy male and female Saudi volunteers living in Riyadh, Saudi Arabia. Four consecutive earwax swab samples were obtained from each volunteer and stored for 1, 15, 30 and 60 days. Earwax samples were stored at room temperature (20–22 °C). Reference oral swab was also taken from each volunteer. DNA was extracted by QIAamp DNA Mini kit and quantified by real-time polymerase chain reaction (RT-PCR) on 7500 Thermal Cycler. Autosomal STR loci were amplified using AmpFLSTR™ Identifiler™ Plus PCR Amplification Kit (Thermo Fisher Scientific, Carlsbad, CA, USA). Amplified fragments were size separated and analyzed on a 3500 Genetic Analyzer. Complete autosomal STR profiles were obtained from the earwax swabs of all the volunteers stored up to 30 days after the collection. Some STR profiles were partially obtained 60 days after the earwax collection. Allelic drop-out, allelic drop-in, and stutters were seen in earwax samples analyzed 60 days after the collection. The results have shown that human earwax can be a potential source of DNA evidence for human identification up to 30 days after the earwax collection. It is recommended to quickly analyze earwax samples or store them at room temperature or at −10 °C after their recovery from the crime scene.
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Kim, Hye Ran, Eun-Jeong Won, Hyun-Jung Choi, Hwan-Young Kim, James Moon, Jong-Hee Shin, Soon-Pal Suh, Dong-Wook Ryang, and Myung-Geun Shin. "Mitochondrial DNA Minisatellites Showed Higher Informativeness and Sensitivity Than the Nuclear DNA Markers for the Quantitative Determination of Chimerism After Allogeneic Stem Cell Transplantation,." Blood 118, no. 21 (November 18, 2011): 4004. http://dx.doi.org/10.1182/blood.v118.21.4004.4004.
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Abstract Abstract 4004 Background: Mitochondrial DNA (mtDNA) is widely used in forensic identification and anthropologic studies on account of its abundance resulting in preferential amplification, sequencing and inherent variability. We developed mtDNA markers to monitor donor cell engraftment after allogeneic stem cell transplantation(SCT), then compared with nuclear short tandem repeat (STR) markers. Patients and methods: The mtDNA control regions and six mtDNA minisatellites (mtMS) (303 poly C, 16184 poly C, 514 (CA) repeat, 3566 poly C, 12385 poly C and 12418 poly A) from the total DNA samples of 215 cases (donor, recipient and after allogeneic SCT) were amplified using the designated specific primers and PCR. The results were compared with those from the six short tandem repeat (STR) markers (D12S391, D18S51, F13A1, HUM RENA-4, HUM FABP2 and Amelogenin). Results: Polymorphisms in the mtDNA control region identify an informative marker in 88% (189 cases) of all cases. Among the six mtMS markers, the informativeness of 303 poly C and 16184 poly C mtMS was 63% and 67% respectively. A combination of direct sequencing through the mtDNA control region, 303poly C and 16184 poly C mtMS could completely distinguish the donor cells from the recipient cells. The results from a typical mixing experiment to determine the sensitivity revealed a detection limit (DL) of the gene scan analysis in a mtDNA mixture to be visible at 1% heteroplasmy in 303 poly C mtMS marker. However, the DL from D12S391 in the same mixing experiment was 5–10% heteroplasmy. Conclusions: mtMS markers, especially 303 poly C and 16184 poly C markers, can provide a sensitive, accurate and quantitative determination of mixed chimerism after a SCT. Disclosures: No relevant conflicts of interest to declare.
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Hindmarsh, Patrick, Michael Johnson, Ray Reeves, and Jonathan Leis. "Base-Pair Substitutions in Avian Sarcoma Virus U5 and U3 Long Terminal Repeat Sequences Alter the Process of DNA Integration In Vitro." Journal of Virology 75, no. 3 (February 1, 2001): 1132–41. http://dx.doi.org/10.1128/jvi.75.3.1132-1141.2001.
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ABSTRACT We have described a reconstituted avian sarcoma virus (ASV) concerted DNA integration system with specially designed mini-donor DNA containing a supF transcription unit, a supercoiled plasmid acceptor, purified bacterially expressed ASV integrase (IN), and human high-mobility-group protein I(Y). Integration in this system is dependent upon the mini-donor DNA having IN recognition sequences at both ends and upon both ends of the same donor integrating into the acceptor DNA. The integrated DNA product exhibits all of the features associated with integration of viral DNA in vivo (P. Hindmarsh et al., J. Virol., 73:2994–3003, 1999). Individual integrants are isolated from bacteria containing drug-resistant markers with amber mutations. This system was used to evaluate the importance of sequences in the terminal U5 and U3 long terminal repeats at positions 5 and/or 6, adjacent to the conserved CA dinucleotide. Base-pair substitutions introduced at these positions in U5 result in significant reductions in recovered integrants from bacteria, due to increases in one-ended insertion events. Among the recovered integrants from reactions with mutated U5 but not U3 IN recognition sequences were products that contain large deletions in the acceptor DNA. Base-pair substitutions at positions 5 and 6 in U3 mostly reduce the efficiency of integration of the modified donor. Together, these results indicate that sequences directly 5′ to the conserved CA dinucleotide are very important for the process of concerted DNA integration. Furthermore, IN interacts with U3 and U5 termini differently, and aberrant end-processing events leading to nonconcerted DNA integration are more common in U5 than in U3.
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Lee, Sook-Kyung, Kunio Nagashima, and Wei-Shau Hu. "Cooperative Effect of Gag Proteins p12 and Capsid during Early Events of Murine Leukemia Virus Replication." Journal of Virology 79, no. 7 (April 1, 2005): 4159–69. http://dx.doi.org/10.1128/jvi.79.7.4159-4169.2005.
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ABSTRACT The Gag polyprotein of murine leukemia virus (MLV) is processed into matrix (MA), p12, capsid (CA), and nucleocapsid (NC) proteins. p12 affects early events of virus replication and contains a PPPY motif important for virus release. To probe the functions of p12 in the early steps of MLV replication, we tested whether p12 can be replaced by spleen necrosis virus (SNV) p18, human immunodeficiency virus type 1 p6, or Rous sarcoma virus p2b. Analyses revealed that all chimeras generated virions at levels similar to that of MLV gag-pol; however, none of them could support MLV vector replication, and all of them exhibited severely reduced DNA synthesis upon virus infection. Because a previously reported SNV gag-MLV pol chimera, but not the MLV hybrid with SNV p18, can support replication of an MLV vector, we hypothesized that other Gag proteins act cooperatively with p12 during the early phase of virus replication. To test this hypothesis, we generated three more MLV-based chimeras containing SNV CA, p18-CA, or p18-CA-NC. We found that the MLV chimera containing SNV p18-CA or p18-CA-NC could support MLV vector replication, but the chimera containing SNV CA could not. Furthermore, viruses derived from the MLV chimera with SNV CA could synthesize viral DNA upon infection but were blocked at a post-reverse-transcription step and generated very little two long terminal repeat circle DNA, thereby producing a phenotype similar to that of the provirus formation-defective p12 mutants. Taken together, our data indicate that when p12/p18 or CA was from different viruses, despite abundant virus production and proper Gag processing, the resulting viruses were not infectious. However, when p12/p18 and CA were from the same virus, even though they were from SNV and not MLV, the resulting viruses were infectious. Therefore, these results suggest a cooperative effect of p12 and CA during the early events of MLV replication.
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Oh, Jangsuk, Kevin W. Chang, and Stephen H. Hughes. "Mutations in the U5 Sequences Adjacent to the Primer Binding Site Do Not Affect tRNA Cleavage by Rous Sarcoma Virus RNase H but Do Cause Aberrant Integrations In Vivo." Journal of Virology 80, no. 1 (January 1, 2006): 451–59. http://dx.doi.org/10.1128/jvi.80.1.451-459.2006.
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ABSTRACT In most retroviruses, the first nucleotide added to the tRNA primer becomes the right end of the U5 region in the right long terminal repeat (LTR); the removal of this tRNA primer by RNase H defines the right end of the linear double-stranded DNA. Most retroviruses have two nucleotides between the 5′ end of the primer binding site (PBS) and the CA dinucleotide that will become the end of the integrated provirus. However, human immunodeficiency virus type 1 (HIV-1) has only one nucleotide at this position, and HIV-2 has three nucleotides. We changed the two nucleotides (TT) between the PBS and the CA dinucleotide of the Rous sarcoma virus (RSV)-derived vector RSVP(A)Z to match the HIV-1 sequence (G) and the HIV-2 sequence (GGT), and we changed the CA dinucleotide to TC. In all three mutants, RNase H removes the entire tRNA primer. Sequence analysis of RSVP(HIV2) proviruses suggests that RSV integrase can remove three nucleotides from the U5 LTR terminus of the linear viral DNA during integration, although this mutation significantly reduced virus titer, suggesting that removing three nucleotides is inefficient. However, the results obtained with RSVP(HIV1) and RSVP(CATC) show that RSV integrase can process and integrate the normal U3 LTR terminus of a linear DNA independently of an aberrant U5 LTR terminus. The aberrant end can then be joined to the host DNA by unusual processes that do not involve the conserved CA dinucleotide. These unusual events generate either large duplications or, less frequently, deletions in the host genomic DNA instead of the normal 5- to 6-base duplications.
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Oh, Jangsuk, Kevin W. Chang, W. Gregory Alvord, and Stephen H. Hughes. "Alternate Polypurine Tracts Affect Rous Sarcoma Virus Integration In Vivo." Journal of Virology 80, no. 20 (October 15, 2006): 10281–84. http://dx.doi.org/10.1128/jvi.00361-06.
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ABSTRACT When the endogenous polypurine tract (PPT) of the Rous sarcoma virus (RSV)-derived vector RSVP(A)Z was replaced with alternate retroviral PPTs, the fraction of unintegrated viral DNA with the normal consensus ends significantly decreased and the retention of part of the PPT significantly increased. If the terminus of the U3 long terminal repeat (LTR) is aberrant, RSV integrase can correctly process and integrate the normal U5 LTR into the host genome. However, the canonical CA is not involved in joining the aberrant U3 LTR to the host DNA, generating either large duplications or deletions of the host sequences instead of the normal 5- or 6-bp duplication.
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Saal, B., and Günter Wricke. "Development of simple sequence repeat markers in rye (Secale cereale L.)." Genome 42, no. 5 (October 1, 1999): 964–72. http://dx.doi.org/10.1139/g99-052.
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Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)n and (GT/CA)n dinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.Key words: simple sequence repeats, microsatellites, mapping, rye, Secale cereale.
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Eide, D. J., and P. Anderson. "Novel insertion mutation in Caenorhabditis elegans." Molecular and Cellular Biology 5, no. 1 (January 1985): 1–6. http://dx.doi.org/10.1128/mcb.5.1.1-6.1985.
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The mutation e1662 is an allele of the Caenorhabditis elegans unc-54 gene induced with the difunctional alkylating agent 1,2,7,8-diepoxyoctane. unc-54 encodes the major myosin heavy chain isozyme of body wall muscle cells. Filter-transfer hybridization and DNA sequence analysis show that e1662 is an insertion of 288 base pairs of DNA within unc-54. The inserted DNA is identical to a 288-base pair region of unc-54 located ca. 600 base pairs from the insertion site. Thus, e1662 is a displaced duplication. A 14-base pair sequence located at one end of the duplicated segment is found adjacent to the site of insertion. These homologous sequences are juxtaposed head-to-tail by the insertion event. e1662 thus contains a tandem direct repeat extending across one of its junctions.
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Eide, D. J., and P. Anderson. "Novel insertion mutation in Caenorhabditis elegans." Molecular and Cellular Biology 5, no. 1 (January 1985): 1–6. http://dx.doi.org/10.1128/mcb.5.1.1.
Full textAbstract:
The mutation e1662 is an allele of the Caenorhabditis elegans unc-54 gene induced with the difunctional alkylating agent 1,2,7,8-diepoxyoctane. unc-54 encodes the major myosin heavy chain isozyme of body wall muscle cells. Filter-transfer hybridization and DNA sequence analysis show that e1662 is an insertion of 288 base pairs of DNA within unc-54. The inserted DNA is identical to a 288-base pair region of unc-54 located ca. 600 base pairs from the insertion site. Thus, e1662 is a displaced duplication. A 14-base pair sequence located at one end of the duplicated segment is found adjacent to the site of insertion. These homologous sequences are juxtaposed head-to-tail by the insertion event. e1662 thus contains a tandem direct repeat extending across one of its junctions.
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Griffiths, Keren K., and Irina M. Russu. "Specific Interactions of Divalent Metal Ions with a DNA Duplex Containing the d(CA)n/(GT)nTandem Repeat." Journal of Biomolecular Structure and Dynamics 23, no. 6 (June 2006): 667–76. http://dx.doi.org/10.1080/07391102.2006.10507091.
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Dismuke, David J., and Christopher Aiken. "Evidence for a Functional Link between Uncoating of the Human Immunodeficiency Virus Type 1 Core and Nuclear Import of the Viral Preintegration Complex." Journal of Virology 80, no. 8 (April 15, 2006): 3712–20. http://dx.doi.org/10.1128/jvi.80.8.3712-3720.2006.
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ABSTRACT Human immunodeficiency virus type 1 (HIV-1) particles begin their replication upon fusion with the plasma membrane of target cells and release of the viral core into the host cell cytoplasm. Soon thereafter, the viral capsid, which is composed of a polymer of the CA protein, disassociates from the internal ribonucleoprotein complex. While this disassembly process remains poorly understood, the available evidence indicates that proper uncoating of the core is a key step in infection. Defects in uncoating most often lead to a failure of the virus to undergo reverse transcription, resulting in an inability to form a functional viral preintegration complex (PIC). In a previous study, we reported that an HIV-1 mutant containing two substitutions in CA (Q63A/67A) was unusual in that it was poorly infectious yet synthesized normal levels of viral DNA. Here we report that this mutant is impaired for nuclear entry. Quantitative analysis of viral DNA synthesis from infected cells by Southern blotting and real-time PCR revealed that the Q63A/Q67A mutant is impaired in the synthesis of one-long terminal repeat (1-LTR) and 2-LTR circles. Isolation of PICs from acutely infected cells revealed that the Q63A/Q67A mutant produces protein-DNA complexes similar to wild-type in yield and overall composition, but these PICs contained elevated levels of CA and were impaired for integration in vitro. These results demonstrate that mutations in CA can have deleterious effects on both nuclear targeting and integration, suggesting that these steps in the HIV-1 life cycle are dependent on proper uncoating of the viral core.
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Hammond, P. W., T. N. Lively, and T. R. Cech. "The anchor site of telomerase from Euplotes aediculatus revealed by photo-cross-linking to single- and double-stranded DNA primers." Molecular and Cellular Biology 17, no. 1 (January 1997): 296–308. http://dx.doi.org/10.1128/mcb.17.1.296.
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Telomerase is a ribonucleoprotein enzyme that adds telomeric sequence repeats to the ends of linear chromosomes. In vitro, telomerase has been observed to add repeats to a DNA oligonucleotide primer in a processive manner, leading to the postulation of a DNA anchor site separate from the catalytic site of the enzyme. We have substituted photoreactive 5-iododeoxypyrimidines into the DNA oligonucleotide primer d(T4G4T4G4T4G2) and, upon irradiation, obtained cross-links with the anchor site of telomerase from Euplotes aediculatus nuclear extract. No cross-linking occurred with a primer having the same 5' end and a nontelomeric 3' end. These cross-links were shown to be between the DNA primer and (i) a protein moiety of approximately 130 kDa and (ii) U51-U52 of the telomerase RNA. The cross-linked primer could be extended by telomerase in the presence of [alpha-32P]dGTP, thus indicating that the 3' end was bound in the enzyme active site. The locations of the cross-links within the single-stranded primers were 20 to 22 nucleotides upstream of the 3' end, providing a measure of the length of DNA required to span the telomerase active and anchor sites. When the single-stranded primers are aligned with the G-rich strand of a Euplotes telomere, the cross-linked nucleotides correspond to the duplex region. Consistent with this finding, a cross-link to telomerase was obtained by substitution of 5-iododeoxycytidine into the CA strand of the duplex region of telomere analogs. We conclude that the anchor site in the approximately 130-kDa protein can bind duplex as well as single-stranded DNA, which may be critical for its function at chromosome ends. Quantitation of the processivity with single-stranded DNA primers and double-stranded primers with 3' tails showed that only 60% of the primer remains bound after each repeat addition.
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D'Ambrosio, E., S. D. Waitzkin, F. R. Witney, A. Salemme, and A. V. Furano. "Structure of the highly repeated, long interspersed DNA family (LINE or L1Rn) of the rat." Molecular and Cellular Biology 6, no. 2 (February 1986): 411–24. http://dx.doi.org/10.1128/mcb.6.2.411-424.1986.
Full textAbstract:
We present the DNA sequence of a 6.7-kilobase member of the rat long interspersed repeated DNA family (LINE or L1Rn). This member (LINE 3) is flanked by a perfect 14-base-pair (bp) direct repeat and is a full-length, or close-to-full-length, member of this family. LINE 3 contains an approximately 100-bp A-rich right end, a number of long (greater than 400-bp) open reading frames, and a ca. 200-bp G + C-rich (ca. 60%) cluster near each terminus. Comparison of the LINE 3 sequence with the sequence of about one-half of another member, which we also present, as well as restriction enzyme analysis of the genomic copies of this family, indicates that in length and overall structure LINE 3 is quite typical of the 40,000 or so other genomic members of this family which would account for as much as 10% of the rat genome. Therefore, the rat LINE family is relatively homogeneous, which contrasts with the heterogeneous LINE families in primates and mice. Transcripts corresponding to the entire LINE sequence are abundant in the nuclear RNA of rat liver. The characteristics of the rat LINE family are discussed with respect to the possible function and evolution of this family of DNA sequences.
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D'Ambrosio, E., S. D. Waitzkin, F. R. Witney, A. Salemme, and A. V. Furano. "Structure of the highly repeated, long interspersed DNA family (LINE or L1Rn) of the rat." Molecular and Cellular Biology 6, no. 2 (February 1986): 411–24. http://dx.doi.org/10.1128/mcb.6.2.411.
Full textAbstract:
We present the DNA sequence of a 6.7-kilobase member of the rat long interspersed repeated DNA family (LINE or L1Rn). This member (LINE 3) is flanked by a perfect 14-base-pair (bp) direct repeat and is a full-length, or close-to-full-length, member of this family. LINE 3 contains an approximately 100-bp A-rich right end, a number of long (greater than 400-bp) open reading frames, and a ca. 200-bp G + C-rich (ca. 60%) cluster near each terminus. Comparison of the LINE 3 sequence with the sequence of about one-half of another member, which we also present, as well as restriction enzyme analysis of the genomic copies of this family, indicates that in length and overall structure LINE 3 is quite typical of the 40,000 or so other genomic members of this family which would account for as much as 10% of the rat genome. Therefore, the rat LINE family is relatively homogeneous, which contrasts with the heterogeneous LINE families in primates and mice. Transcripts corresponding to the entire LINE sequence are abundant in the nuclear RNA of rat liver. The characteristics of the rat LINE family are discussed with respect to the possible function and evolution of this family of DNA sequences.
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Stringer, J. R. "Recombination between poly[d(GT).d(CA)] sequences in simian virus 40-infected cultured cells." Molecular and Cellular Biology 5, no. 6 (June 1985): 1247–59. http://dx.doi.org/10.1128/mcb.5.6.1247-1259.1985.
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CVI cells were transfected with oversized simian virus 40 (SV40) genomes that could be reduced to packageable size by alternative homologous recombination pathways involving either two polydeoxyguanylic-thymidylic acid X polydeoxycytidylic-adenylic acid (poly[d(GT).d(CA)]; abbreviated hereafter as poly(GT)] tracts or two tracts of homologous SV40 sequence. Plaque-forming viruses rescued by this procedure were found to contain genomes formed by homologous and nonhomologous recombination events. Half of the viable viral DNA molecules recovered were the result of recombination between two tracts of poly(GT). Approximately 20% of the rescued viral genomes were produced by homologous recombination between tracts of SV40 DNA. Nonhomologous recombination involving SV40 sequences was also a major pathway of deletion, producing ca. 30% of the viral plaques. Tracts of poly(GT) generated by recombination were variable in length, suggesting that recombination between poly(GT) tracts was usually unequal. On a per-nucleotide basis, poly(GT) recombination occurred eight times more frequently than did recombination between homologous SV40 DNA. This eightfold difference is the maximum recombinatory enhancement attributable to poly(GT) sequences. Although DNA sequence analysis showed that tracts of poly(GT) generated by recombination retained the alternating G-T repeat motif throughout their length, the contribution of the nonhomologous pathway to poly(GT) recombination cannot be ruled out, and the relative proclivity of a given length of d(GT).d(CA) sequence to undergo homologous recombination is probably less than eight times greater than that of an SV40 sequence of the same length.
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Stringer, J. R. "Recombination between poly[d(GT).d(CA)] sequences in simian virus 40-infected cultured cells." Molecular and Cellular Biology 5, no. 6 (June 1985): 1247–59. http://dx.doi.org/10.1128/mcb.5.6.1247.
Full textAbstract:
CVI cells were transfected with oversized simian virus 40 (SV40) genomes that could be reduced to packageable size by alternative homologous recombination pathways involving either two polydeoxyguanylic-thymidylic acid X polydeoxycytidylic-adenylic acid (poly[d(GT).d(CA)]; abbreviated hereafter as poly(GT)] tracts or two tracts of homologous SV40 sequence. Plaque-forming viruses rescued by this procedure were found to contain genomes formed by homologous and nonhomologous recombination events. Half of the viable viral DNA molecules recovered were the result of recombination between two tracts of poly(GT). Approximately 20% of the rescued viral genomes were produced by homologous recombination between tracts of SV40 DNA. Nonhomologous recombination involving SV40 sequences was also a major pathway of deletion, producing ca. 30% of the viral plaques. Tracts of poly(GT) generated by recombination were variable in length, suggesting that recombination between poly(GT) tracts was usually unequal. On a per-nucleotide basis, poly(GT) recombination occurred eight times more frequently than did recombination between homologous SV40 DNA. This eightfold difference is the maximum recombinatory enhancement attributable to poly(GT) sequences. Although DNA sequence analysis showed that tracts of poly(GT) generated by recombination retained the alternating G-T repeat motif throughout their length, the contribution of the nonhomologous pathway to poly(GT) recombination cannot be ruled out, and the relative proclivity of a given length of d(GT).d(CA) sequence to undergo homologous recombination is probably less than eight times greater than that of an SV40 sequence of the same length.
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Ge, Jing, Cheng-Ao Yang, Jia-Yi Wu, and Jia-Yu Xue. "Mitochondrial Genomes of Hibiscus Reveal Structural Heterogeneity and Phylogenetic Relationships." Horticulturae 11, no. 3 (February 20, 2025): 225. https://doi.org/10.3390/horticulturae11030225.
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Hibiscus, which belongs to the Malvaceae family, is primarily distributed in tropical and subtropical regions. Hibiscus species are known for their large, visually striking flowers, which are highly valued for ornamental purposes and are widely admired. Despite this diversity, the mitochondrial DNA of Hibiscus species remains largely unexplored. Here, we assembled chromosome-level mitochondrial genomes (mitogenomes) of H. schizopetalus, H. syriacus, H. hamabo, and Talipariti tiliaceum (Hibiscus tiliaceum) using Illumina short reads (Illumina, Inc., San Diego, CA, USA) and PacBio long reads (Pacific Biosciences of California, Inc., Menlo Park, CA, USA), and conducted comparative genomic analyses. Our findings revealed that the mitogenomes of Hibiscus species exhibited structural complexity, including variable sizes and multi-molecular configurations, while maintaining high conservation in codon usage bias and GC content. Repeat sequence analysis suggested that repeat-mediated homologous recombination played a critical role in frequent recombination events in the mitogenomes. In addition, phylogenetic analysis showed that Hibiscus species did not form a monophyletic clade, and H. hamabo and T. tiliaceum were positioned in sister clades, which was consistent with the results of synteny analysis. To sum up, our study provides valuable resources for phylogenetic research and makes significant contributions to exploring further genetic mechanisms and biodiversity of Hibiscus species.