1
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De Rache A, Marquevielle J, Bouaziz S, Vialet B, Andreola ML, Mergny JL, Amrane S. Structure of a DNA G-quadruplex that Modulates SP1 Binding Sites Architecture in HIV-1 Promoter. J Mol Biol 2024; 436:168359. [PMID: 37952768 DOI: 10.1016/j.jmb.2023.168359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Nucleic acid sequences containing guanine tracts are able to form non-canonical DNA or RNA structures known as G-quadruplexes (or G4s). These structures, based on the stacking of G-tetrads, are involved in various biological processes such as gene expression regulation. Here, we investigated a G4 forming sequence, HIVpro2, derived from the HIV-1 promoter. This motif is located 60 nucleotides upstream of the proviral Transcription Starting Site (TSS) and overlaps with two SP1 transcription factor binding sites. Using NMR spectroscopy, we determined that HIVpro2 forms a hybrid type G4 structure with a core that is interrupted by a single nucleotide bulge. An additional reverse-Hoogsteen AT base pair is stacked on top of the tetrad. SP1 transcription factor is known to regulate transcription activity of many genes through the recognition of Guanine-rich duplex motifs. Here, the formation of HIVpro2 G4 may modulate SP1 binding sites architecture by competing with the formation of the canonical duplex structure. Such DNA structural switch potentially participates to the regulation of viral transcription and may also interfere with HIV-1 reactivation or viral latency.
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Affiliation(s)
- Aurore De Rache
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France; Department of Chemistry, U. Namur, 61 rue de Bruxelles, B5000 Namur, Belgium
| | - Julien Marquevielle
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | | | - Brune Vialet
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Marie-Line Andreola
- Université de Bordeaux, Bordeaux, France; MFP Laboratory, UMR5234, CNRS, Bordeaux, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique & Biosciences, École Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Samir Amrane
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France.
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2
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Revisiting mutagenesis at non-B DNA motifs in the human genome. Nat Struct Mol Biol 2023; 30:417-424. [PMID: 36914796 DOI: 10.1038/s41594-023-00936-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/03/2023] [Indexed: 03/16/2023]
Abstract
Non-B DNA structures formed by repetitive sequence motifs are known instigators of mutagenesis in experimental systems. Analyzing this phenomenon computationally in the human genome requires careful disentangling of intrinsic confounding factors, including overlapping and interrupted motifs and recurrent sequencing errors. Here, we show that accounting for these factors eliminates all signals of repeat-induced mutagenesis that extend beyond the motif boundary, and eliminates or dramatically shrinks the magnitude of mutagenesis within some motifs, contradicting previous reports. Mutagenesis not attributable to artifacts revealed several biological mechanisms. Polymerase slippage generates frequent indels within every variety of short tandem repeat motif, implicating slipped-strand structures. Interruption-correcting single nucleotide variants within short tandem repeats may originate from error-prone polymerases. Secondary-structure formation promotes single nucleotide variants within palindromic repeats and duplications within direct repeats. G-quadruplex motifs cause recurrent sequencing errors, whereas mutagenesis at Z-DNAs is conspicuously absent.
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3
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Qi M, Stenson PD, Ball EV, Tainer JA, Bacolla A, Kehrer-Sawatzki H, Cooper DN, Zhao H. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat 2021; 43:328-346. [PMID: 34918412 PMCID: PMC9069542 DOI: 10.1002/humu.24314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022]
Abstract
Microdeletions and gross deletions are important causes (~20%) of human inherited disease and their genomic locations are strongly influenced by the local DNA sequence environment. This notwithstanding, no study has systematically examined their underlying generative mechanisms. Here, we obtained 42,098 pathogenic microdeletions and gross deletions from the Human Gene Mutation Database (HGMD) that together form a continuum of germline deletions ranging in size from 1 to 28,394,429 bp. We analyzed the DNA sequence within 1 kb of the breakpoint junctions and found that the frequencies of non‐B DNA‐forming repeats, GC‐content, and the presence of seven of 78 specific sequence motifs in the vicinity of pathogenic deletions correlated with deletion length for deletions of length ≤30 bp. Further, we found that the presence of DR, GQ, and STR repeats is important for the formation of longer deletions (>30 bp) but not for the formation of shorter deletions (≤30 bp) while significantly (χ2, p < 2E−16) more microhomologies were identified flanking short deletions than long deletions (length >30 bp). We provide evidence to support a functional distinction between microdeletions and gross deletions. Finally, we propose that a deletion length cut‐off of 25–30 bp may serve as an objective means to functionally distinguish microdeletions from gross deletions.
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Affiliation(s)
- Mengling Qi
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
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4
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Impact of G-Quadruplexes and Chronic Inflammation on Genome Instability: Additive Effects during Carcinogenesis. Genes (Basel) 2021; 12:genes12111779. [PMID: 34828385 PMCID: PMC8619830 DOI: 10.3390/genes12111779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
Genome instability is an enabling characteristic of cancer, essential for cancer cell evolution. Hotspots of genome instability, from small-scale point mutations to large-scale structural variants, are associated with sequences that potentially form non-B DNA structures. G-quadruplex (G4) forming motifs are enriched at structural variant endpoints in cancer genomes. Chronic inflammation is a physiological state underlying cancer development, and oxidative DNA damage is commonly invoked to explain how inflammation promotes genome instability. We summarize where G4s and oxidative stress overlap, with a focus on DNA replication. Guanine has low ionization potential, making G4s vulnerable to oxidative damage. Impacts to G4 structure are dependent upon lesion type, location, and G4 conformation. Occasionally, G4s pose a challenge to replicative DNA polymerases, requiring specialized DNA polymerases to maintain genome stability. Therefore, chronic inflammation creates a dual challenge for DNA polymerases to maintain genome stability: faithful G4 synthesis and bypassing unrepaired oxidative lesions. Inflammation is also accompanied by global transcriptome changes that may impact mutagenesis. Several studies suggest a regulatory role for G4s within cancer- and inflammatory-related gene promoters. We discuss the extent to which inflammation could influence gene regulation by G4s, thereby impacting genome instability, and highlight key areas for new investigation.
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5
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Brázda V, Bartas M, Bowater RP. Evolution of Diverse Strategies for Promoter Regulation. Trends Genet 2021; 37:730-744. [PMID: 33931265 DOI: 10.1016/j.tig.2021.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022]
Abstract
DNA is fundamentally important for all cellular organisms due to its role as a store of hereditary genetic information. The precise and accurate regulation of gene transcription depends primarily on promoters, which vary significantly within and between genomes. Some promoters are rich in specific types of bases, while others have more varied, complex sequence characteristics. However, it is not only base sequence but also epigenetic modifications and altered DNA structure that regulate promoter activity. Significantly, many promoters across all organisms contain sequences that can form intrastrand hairpins (cruciforms) or four-stranded structures (G-quadruplex or i-motif). In this review we integrate recent studies on promoter regulation that highlight the importance of DNA structure in the evolutionary adaptation of promoter sequences.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Richard P Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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6
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Lei H, Lu Q, Xiang D, Wang X, Cai X. ABO gene mutation c.815_816insG in an African individual forms a novel A el allele. Transfusion 2021; 61:E51-E52. [PMID: 33899249 DOI: 10.1111/trf.16419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Hang Lei
- Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
| | - Qiong Lu
- Blood Group Reference Laboratory, Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Dong Xiang
- Blood Group Reference Laboratory, Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Xuefeng Wang
- Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
| | - Xiaohong Cai
- Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
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7
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Guiblet WM, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Res 2021; 49:1497-1516. [PMID: 33450015 PMCID: PMC7897504 DOI: 10.1093/nar/gkaa1269] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, UniversityPark, PA 16802, USA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Operations and Decision Systems, Université Laval, Canada
- CHU de Québec – Université Laval Research Center, Canada
| | - Robert S Harris
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Di Chen
- Intercollege Graduate Degree Program in Genetics, Huck Institutes of the Life Sciences, Penn State University, UniversityPark, PA 16802, USA
| | - Kristin A Eckert
- Department of Pathology, Penn State University, College of Medicine, Hershey, PA 17033, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
- EMbeDS, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
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8
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Wang Q, Pierce-Hoffman E, Cummings BB, Alföldi J, Francioli LC, Gauthier LD, Hill AJ, O'Donnell-Luria AH, Karczewski KJ, MacArthur DG. Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes. Nat Commun 2020; 11:2539. [PMID: 32461613 PMCID: PMC7253413 DOI: 10.1038/s41467-019-12438-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/09/2019] [Indexed: 12/31/2022] Open
Abstract
Multi-nucleotide variants (MNVs), defined as two or more nearby variants existing on the same haplotype in an individual, are a clinically and biologically important class of genetic variation. However, existing tools typically do not accurately classify MNVs, and understanding of their mutational origins remains limited. Here, we systematically survey MNVs in 125,748 whole exomes and 15,708 whole genomes from the Genome Aggregation Database (gnomAD). We identify 1,792,248 MNVs across the genome with constituent variants falling within 2 bp distance of one another, including 18,756 variants with a novel combined effect on protein sequence. Finally, we estimate the relative impact of known mutational mechanisms - CpG deamination, replication error by polymerase zeta, and polymerase slippage at repeat junctions - on the generation of MNVs. Our results demonstrate the value of haplotype-aware variant annotation, and refine our understanding of genome-wide mutational mechanisms of MNVs.
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Affiliation(s)
- Qingbo Wang
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, 02115, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Beryl B Cummings
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Biomedical and Biological Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Jessica Alföldi
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Laurent C Francioli
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew J Hill
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia.
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9
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Seo SH, Bacolla A, Yoo D, Koo YJ, Cho SI, Kim MJ, Seong MW, Kim HJ, Kim JM, Tainer JA, Park SS, Kim JY, Jeon B. Replication-Based Rearrangements Are a Common Mechanism for SNCA Duplication in Parkinson's Disease. Mov Disord 2020; 35:868-876. [PMID: 32039503 DOI: 10.1002/mds.27998] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND SNCA multiplication is a genomic cause of familial PD, showing dosage-dependent toxicity. Until now, nonallelic homologous recombination was suggested as the mechanism of SNCA duplication, based on various types of repetitive elements found in the spanning region of the breakpoints. However, the sequence at the breakpoint was analyzed only for 1 case. OBJECTIVES We have analyzed the breakpoint sequences of 6 patients with PD who had duplicated SNCA using whole-genome sequencing data to elucidate the mechanism of SNCA duplication. METHODS Six patient samples with SNCA duplication underwent whole-genome sequencing. The duplicated regions were defined with nucleotide-resolution breakpoints, which were confirmed by junction polymerase chain reaction and Sanger sequencing. The search for potential non-B DNA-forming sequences and stem-loop structure predictions was conducted. RESULTS Duplicated regions ranged from the smallest region of 718.3 kb to the largest one of 4,162 kb. Repetitive elements were found at 8 of the 12 breakpoint sequences on each side of the junction, but none of the pairs shared overt homologies. Five of these six junctions had microhomologies (2-4 bp) at the breakpoint, and a short stretch of sequences was inserted in 3 cases. All except one junction were located within or next to stem-loop structures. CONCLUSION Our study has determined that homologous recombination mechanisms involving repetitive elements are not the main cause of the duplication of SNCA. The presence of microhomology at the junctions and their position within stem-loop structures suggest that replication-based rearrangements may be a common mechanism for SNCA amplification. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Seoul National University College of Medicine, Seoul, Korea
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dallah Yoo
- Department of Neurology, Kyung Hee University Hospital, Seoul, Korea
| | - Yoon Jung Koo
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Han-Joon Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Min Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sung Sup Park
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Ji Yeon Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Beomseok Jeon
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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10
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017. [PMID: 28349240 DOI: 10.1007/s00439‐017‐1779‐6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD ( http://www.hgmd.org ) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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11
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017; 136:665-677. [PMID: 28349240 PMCID: PMC5429360 DOI: 10.1007/s00439-017-1779-6] [Citation(s) in RCA: 912] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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12
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Bacolla A, Tainer JA, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res 2016; 44:5673-88. [PMID: 27084947 PMCID: PMC4937311 DOI: 10.1093/nar/gkw261] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes and often create oncogenic fusion genes. An obligate step in the generation of such gross rearrangements is the formation of DNA double-strand breaks (DSBs). Since the genomic distribution of rearrangement breakpoints is non-random, intrinsic cellular factors may predispose certain genomic regions to breakage. Notably, certain DNA sequences with the potential to fold into secondary structures [potential non-B DNA structures (PONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structures with implications in DNA replication and transcription] can stimulate the formation of DNA DSBs. Here, we tested the postulate that these DNA sequences might be found at, or in close proximity to, rearrangement breakpoints. By analyzing the distribution of PONDS-forming sequences within ±500 bases of 19 947 translocation and 46 365 sequence-characterized deletion breakpoints in cancer genomes, we find significant association between PONDS-forming repeats and cancer breakpoints. Specifically, (AT)n, (GAA)n and (GAAA)n constitute the most frequent repeats at translocation breakpoints, whereas A-tracts occur preferentially at deletion breakpoints. Translocation breakpoints near PONDS-forming repeats also recur in different individuals and patient tumor samples. Hence, PONDS-forming sequences represent an intrinsic risk factor for genomic rearrangements in cancer genomes.
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Affiliation(s)
- Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Curr Opin Struct Biol 2016; 37:29-45. [DOI: 10.1016/j.sbi.2015.11.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/05/2023]
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Kamat MA, Bacolla A, Cooper DN, Chuzhanova N. A Role for Non-B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease. Hum Mutat 2015; 37:65-73. [PMID: 26466920 DOI: 10.1002/humu.22917] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/22/2015] [Indexed: 12/25/2022]
Abstract
Missense/nonsense mutations and microdeletions/microinsertions (<21 bp) represent ∼ 76% of all mutations causing human inherited disease, and their occurrence has been associated with sequence motifs (direct, inverted, and mirror repeats; G-quartets) capable of adopting non-B DNA structures. We found that a significant proportion (∼ 21%) of both microdeletions and microinsertions occur within direct repeats, and are explicable by slipped misalignment. A novel mutational mechanism, DNA triplex formation followed by DNA repair, may explain ∼ 5% of microdeletions and microinsertions at mirror repeats. Further, G-quartets, direct, and inverted repeats also appear to play a prominent role in mediating missense mutations, whereas only direct and inverted repeats mediate nonsense mutations. We suggest a mutational mechanism involving slipped strand mispairing, slipped structure formation, and DNA repair, to explain ∼ 15% of missense and ∼ 12% of nonsense mutations yielding perfect direct repeats from imperfect repeats, or the extension of existing direct repeats. Similar proportions of missense and nonsense mutations were explicable by hairpin/loop formation and DNA repair, yielding perfect inverted repeats from imperfect repeats. We also propose a model for single base-pair substitution based on one-electron oxidation reactions at G-quadruplex DNA. Overall, the proposed mechanisms provide support for a role for non-B DNA structures in human gene mutagenesis.
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Affiliation(s)
- Mihir Anant Kamat
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, UK
| | - Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Nadia Chuzhanova
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, UK
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Temiz NA, Donohue DE, Bacolla A, Vasquez KM, Cooper DN, Mudunuri U, Ivanic J, Cer RZ, Yi M, Stephens RM, Collins JR, Luke BT. The somatic autosomal mutation matrix in cancer genomes. Hum Genet 2015; 134:851-64. [PMID: 26001532 PMCID: PMC4495249 DOI: 10.1007/s00439-015-1566-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/12/2015] [Indexed: 01/26/2023]
Abstract
DNA damage in somatic cells originates from both environmental and endogenous sources, giving rise to mutations through multiple mechanisms. When these mutations affect the function of critical genes, cancer may ensue. Although identifying genomic subsets of mutated genes may inform therapeutic options, a systematic survey of tumor mutational spectra is required to improve our understanding of the underlying mechanisms of mutagenesis involved in cancer etiology. Recent studies have presented genome-wide sets of somatic mutations as a 96-element vector, a procedure that only captures the immediate neighbors of the mutated nucleotide. Herein, we present a 32 × 12 mutation matrix that captures the nucleotide pattern two nucleotides upstream and downstream of the mutation. A somatic autosomal mutation matrix (SAMM) was constructed from tumor-specific mutations derived from each of 909 individual cancer genomes harboring a total of 10,681,843 single-base substitutions. In addition, mechanistic template mutation matrices (MTMMs) representing oxidative DNA damage, ultraviolet-induced DNA damage, (5m)CpG deamination, and APOBEC-mediated cytosine mutation, are presented. MTMMs were mapped to the individual tumor SAMMs to determine the maximum contribution of each mutational mechanism to the overall mutation pattern. A Manhattan distance across all SAMM elements between any two tumor genomes was used to determine their relative distance. Employing this metric, 89.5% of all tumor genomes were found to have a nearest neighbor from the same tissue of origin. When a distance-dependent 6-nearest neighbor classifier was used, 10.4% of the SAMMs had an Undetermined tissue of origin, and 92.2% of the remaining SAMMs were assigned to the correct tissue of origin. [corrected]. Thus, although tumors from different tissues may have similar mutation patterns, their SAMMs often display signatures that are characteristic of specific tissues.
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Affiliation(s)
- Nuri A. Temiz
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Masonic Cancer Center, University of Minnesota, 2-120 CCRB, 2231 6th St SE, Minneapolis, MN 55455 USA
| | - Duncan E. Donohue
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />US Army Medical Research and Material Command, 568 Doughten Dr., Fort Detrick, Frederick, MD 21702 USA
| | - Albino Bacolla
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Division of Pharmacology and Toxicology, The University of Texas at Austin, Austin, TX 78723 USA
| | - Karen M. Vasquez
- />Division of Pharmacology and Toxicology, The University of Texas at Austin, Austin, TX 78723 USA
| | - David N. Cooper
- />Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Uma Mudunuri
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Joseph Ivanic
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Regina Z. Cer
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, Frederick, MD 21702 USA
| | - Ming Yi
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Robert M. Stephens
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Jack R. Collins
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Brian T. Luke
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
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