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Wright GM, Menzel J, Tatman PD, Black JC. Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539886. [PMID: 37214911 PMCID: PMC10197558 DOI: 10.1101/2023.05.08.539886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.
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Pascarella G, Frith M, Carninci P. A new layer of complexity in the human genome: Somatic recombination of repeat elements. Clin Transl Med 2023; 13:e1226. [PMID: 36941762 PMCID: PMC10028047 DOI: 10.1002/ctm2.1226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Affiliation(s)
| | - Martin Frith
- Artificial Intelligence Research CenterNational Institute of Advanced Industrial Science and Technology (AIST)TokyoJapan
- Graduate School of Frontier SciencesUniversity of TokyoChibaJapan
- Computational Bio Big‐Data Open Innovation Laboratory (CBBD‐OIL)AISTTokyoJapan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS)YokohamaJapan
- Human TechnopoleMilanItaly
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Datta S, Patel M, Kashyap S, Patel D, Singh U. Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1. Oncotarget 2022; 13:136-155. [PMID: 35070079 PMCID: PMC8765472 DOI: 10.18632/oncotarget.28174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.
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Affiliation(s)
- Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Manthan Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - Sukesh Kashyap
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Divyesh Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Current address: Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki 00290, Finland
| | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing. PLoS One 2020; 15:e0226340. [PMID: 31940362 PMCID: PMC6961855 DOI: 10.1371/journal.pone.0226340] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/25/2019] [Indexed: 12/29/2022] Open
Abstract
Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation.
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Hua Z, Doroodian P, Vu W. Contrasting duplication patterns reflect functional diversities of ubiquitin and ubiquitin-like protein modifiers in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:296-311. [PMID: 29738099 DOI: 10.1111/tpj.13951] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 03/29/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Ubiquitin (Ub) and Ub-like proteins, collectively forming the ubiquiton family, regulate nearly all aspects of cellular processes via post-translational modifications. Studies devoted to specific members suggested a large expansion of this family in plants; however, a lack of systematic analysis hinders the comparison of individual members at both evolutionary history and functional divergence levels, which may provide new insight into biological functions. In this work, we first retrieved a total of 5856 members of 17 known ubiquiton subfamilies in 50 plant genomes by searching both prior annotations and missing loci in each genome. We then applied this list to analyze the duplication history of major ubiquiton subfamilies in plants. We show that autophagy-related protein 8 (ATG8), membrane-anchored Ub-fold (MUB), small Ub-like modifier (SUMO) and Ub loci encode 88% of the plant ubiquiton family. Although whole genome duplications (WGDs) significantly expanded the family, we discovered contrasting duplication patterns both in species and in subfamilies. Within the family, the ATG8 and MUB members were primarily duplicated through WGDs, whereas a significant number of Ub and SUMO loci were generated through retroposition and tandem duplications, respectively. Although Ub coding regions are highly conserved in plants, promoter activity analysis demonstrated lineage-specific expression patterns of polyUb genes in Oryza sativa (rice) and Arabidopsis, confirming their retroposition origin. Based on the theory of dosage balance constraints, our study suggests that ubiquiton members duplicated through WGDs play crucial roles in plants, and that the regulatory pathways involving ATG8 and MUB are more conserved than those controlled by Ub and SUMO.
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Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, 45701, USA
| | - Paymon Doroodian
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - William Vu
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
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Alekseeva LA, Mironova NL, Brenner EV, Kurilshikov AM, Patutina OA, Zenkova MA. Alteration of the exDNA profile in blood serum of LLC-bearing mice under the decrease of tumour invasion potential by bovine pancreatic DNase I treatment. PLoS One 2017; 12:e0171988. [PMID: 28222152 PMCID: PMC5319761 DOI: 10.1371/journal.pone.0171988] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
Taking into account recently obtained data indicating the participation of circulating extracellular DNA (exDNA) in tumorigenesis, enzymes with deoxyribonucleic activity have again been considered as potential antitumour and antimetastatic drugs. Previously, using murine Lewis lung carcinoma and hepatocellular carcinoma A1 tumour models, we have shown the antimetastatic activity of bovine DNase I, which correlates with an increase of DNase activity and a decrease of exDNA concentration in the blood serum of tumour-bearing mice. In this work, using next-generation sequencing on the ABS SOLiD™ 5.500 platform, we performed a search for molecular targets of DNase I by comparing the exDNA profiles of healthy animals, untreated animals with Lewis lung carcinoma (LLC) and those with LLC treated with DNase I. We found that upon DNase I treatment of LLC-bearing mice, together with inhibition of metastasis, a number of strong alterations in the patterns of exDNA were observed. The major differences in exDNA profiles between groups were: i) the level of GC-poor sequences increased during tumour development was reduced to that of healthy mice; ii) levels of sequences corresponding to tumour-associated genes Hmga2, Myc and Jun were reduced in the DNase I-treated group in comparison with non-treated mice; iii) 224 types of tandem repeat over-presented in untreated LLC-bearing mice were significantly reduced after DNase I treatment. The most important result obtained in the work is that DNase I decreased the level of B-subfamily repeats having homology to human ALU repeats, known as markers of carcinogenesis, to the level of healthy animals. Thus, the obtained data lead us to suppose that circulating exDNA plays a role in tumour dissemination, and alteration of multiple molecular targets in the bloodstream by DNase I reduces the invasive potential of tumours.
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Affiliation(s)
- Ludmila A. Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Nadezhda L. Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Evgenyi V. Brenner
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | | | - Olga A. Patutina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
- * E-mail:
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Morales ME, Derbes RS, Ade CM, Ortego JC, Stark J, Deininger PL, Roy-Engel AM. Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes. PLoS One 2016. [PMID: 26966913 DOI: 10.1371/journal.pone.0151367]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs) as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR) and single strand annealing (SSA), which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the "error prone" non-homologous end joining (alt-NHEJ) while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.
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Affiliation(s)
- Maria E Morales
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Rebecca S Derbes
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Catherine M Ade
- Department of Cellular and Molecular Biology, Tulane University, 6400 Freret Street, New Orleans, LA 70118, United States of America
| | - Jonathan C Ortego
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Jeremy Stark
- Department of Radiation Biology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, United States of America
| | - Prescott L Deininger
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Astrid M Roy-Engel
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
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Morales ME, Derbes RS, Ade CM, Ortego JC, Stark J, Deininger PL, Roy-Engel AM. Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes. PLoS One 2016; 11:e0151367. [PMID: 26966913 PMCID: PMC4788447 DOI: 10.1371/journal.pone.0151367] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/26/2016] [Indexed: 11/22/2022] Open
Abstract
Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs) as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR) and single strand annealing (SSA), which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the “error prone” non-homologous end joining (alt-NHEJ) while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.
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Affiliation(s)
- Maria E. Morales
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Rebecca S. Derbes
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Catherine M. Ade
- Department of Cellular and Molecular Biology, Tulane University, 6400 Freret Street, New Orleans, LA 70118, United States of America
| | - Jonathan C. Ortego
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Jeremy Stark
- Department of Radiation Biology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, United States of America
| | - Prescott L. Deininger
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Astrid M. Roy-Engel
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
- * E-mail:
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Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M. Lack of major genome instability in tumors of p53 null rats. PLoS One 2015; 10:e0122066. [PMID: 25811670 PMCID: PMC4374866 DOI: 10.1371/journal.pone.0122066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 02/11/2015] [Indexed: 01/20/2023] Open
Abstract
Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.
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Affiliation(s)
- Roel Hermsen
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Pim Toonen
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ewart Kuijk
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sameh A. Youssef
- Dutch Molecular Pathology Center. Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Raoul Kuiper
- Dutch Molecular Pathology Center. Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Sebastiaan van Heesch
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Alain de Bruin
- Dutch Molecular Pathology Center. Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- * E-mail:
| | - Marieke Simonis
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Cook GW, Konkel MK, Walker JA, Bourgeois MG, Fullerton ML, Fussell JT, Herbold HD, Batzer MA. A comparison of 100 human genes using an alu element-based instability model. PLoS One 2013; 8:e65188. [PMID: 23755193 PMCID: PMC3670932 DOI: 10.1371/journal.pone.0065188] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/23/2013] [Indexed: 02/07/2023] Open
Abstract
The human retrotransposon with the highest copy number is the Alu element. The human genome contains over one million Alu elements that collectively account for over ten percent of our DNA. Full-length Alu elements are randomly distributed throughout the genome in both forward and reverse orientations. However, full-length widely spaced Alu pairs having two Alus in the same (direct) orientation are statistically more prevalent than Alu pairs having two Alus in the opposite (inverted) orientation. The cause of this phenomenon is unknown. It has been hypothesized that this imbalance is the consequence of anomalous inverted Alu pair interactions. One proposed mechanism suggests that inverted Alu pairs can ectopically interact, exposing both ends of each Alu element making up the pair to a potential double-strand break, or "hit". This hypothesized "two-hit" (two double-strand breaks) potential per Alu element was used to develop a model for comparing the relative instabilities of human genes. The model incorporates both 1) the two-hit double-strand break potential of Alu elements and 2) the probability of exon-damaging deletions extending from these double-strand breaks. This model was used to compare the relative instabilities of 50 deletion-prone cancer genes and 50 randomly selected genes from the human genome. The output of the Alu element-based genomic instability model developed here is shown to coincide with the observed instability of deletion-prone cancer genes. The 50 cancer genes are collectively estimated to be 58% more unstable than the randomly chosen genes using this model. Seven of the deletion-prone cancer genes, ATM, BRCA1, FANCA, FANCD2, MSH2, NCOR1 and PBRM1, were among the most unstable 10% of the 100 genes analyzed. This algorithm may lay the foundation for comparing genetic risks posed by structural variations that are unique to specific individuals, families and people groups.
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Affiliation(s)
- George W. Cook
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Miriam K. Konkel
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Matthew G. Bourgeois
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Mitchell L. Fullerton
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| | - John T. Fussell
- Electrochemical Materials, Louisiana Business and Technology Center, Baton Rouge, Louisiana, United States of America
| | - Heath D. Herbold
- Albemarle Corporation, Pasadena, Texas, United States of America
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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