51
|
Wilkins JF, Cannataro VL, Shuch B, Townsend JP. Analysis of mutation, selection, and epistasis: an informed approach to cancer clinical trials. Oncotarget 2018; 9:22243-22253. [PMID: 29854275 PMCID: PMC5976461 DOI: 10.18632/oncotarget.25155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/02/2018] [Indexed: 12/30/2022] Open
Abstract
Currently, drug development efforts and clinical trials to test them are often prioritized by targeting genes with high frequencies of somatic variants among tumors. However, differences in oncogenic mutation rate-not necessarily the effect the variant has on tumor growth-contribute enormously to somatic variant frequency. We argue that decoupling the contributions of mutation and cancer lineage selection to the frequency of somatic variants among tumors is critical to understanding-and predicting-the therapeutic potential of different interventions. To provide an indicator of that strength of selection and therapeutic potential, the frequency at which we observe a given variant across patients must be modulated by our expectation given the mutation rate and target size to provide an indicator of that strength of selection and therapeutic potential. Additionally, antagonistic and synergistic epistasis among mutations also impacts the potential therapeutic benefit of targeted drug development. Quantitative approaches should be fostered that use the known genetic architectures of cancer types, decouple mutation rate, and provide rigorous guidance regarding investment in targeted drug development. By integrating evolutionary principles and detailed mechanistic knowledge into those approaches, we can maximize our ability to identify those targeted therapies most likely to yield substantial clinical benefit.
Collapse
Affiliation(s)
| | | | - Brian Shuch
- Department of Urology, Yale School of Medicine, New Haven, CT, USA
- Department of Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| |
Collapse
|
52
|
Bertl J, Guo Q, Juul M, Besenbacher S, Nielsen MM, Hornshøj H, Pedersen JS, Hobolth A. A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data. BMC Bioinformatics 2018; 19:147. [PMID: 29673314 PMCID: PMC5909259 DOI: 10.1186/s12859-018-2141-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 03/27/2018] [Indexed: 01/02/2023] Open
Abstract
Background Detailed modelling of the neutral mutational process in cancer cells is crucial for identifying driver mutations and understanding the mutational mechanisms that act during cancer development. The neutral mutational process is very complex: whole-genome analyses have revealed that the mutation rate differs between cancer types, between patients and along the genome depending on the genetic and epigenetic context. Therefore, methods that predict the number of different types of mutations in regions or specific genomic elements must consider local genomic explanatory variables. A major drawback of most methods is the need to average the explanatory variables across the entire region or genomic element. This procedure is particularly problematic if the explanatory variable varies dramatically in the element under consideration. Results To take into account the fine scale of the explanatory variables, we model the probabilities of different types of mutations for each position in the genome by multinomial logistic regression. We analyse 505 cancer genomes from 14 different cancer types and compare the performance in predicting mutation rate for both regional based models and site-specific models. We show that for 1000 randomly selected genomic positions, the site-specific model predicts the mutation rate much better than regional based models. We use a forward selection procedure to identify the most important explanatory variables. The procedure identifies site-specific conservation (phyloP), replication timing, and expression level as the best predictors for the mutation rate. Finally, our model confirms and quantifies certain well-known mutational signatures. Conclusion We find that our site-specific multinomial regression model outperforms the regional based models. The possibility of including genomic variables on different scales and patient specific variables makes it a versatile framework for studying different mutational mechanisms. Our model can serve as the neutral null model for the mutational process; regions that deviate from the null model are candidates for elements that drive cancer development. Electronic supplementary material The online version of this article (10.1186/s12859-018-2141-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Johanna Bertl
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark.
| | - Qianyun Guo
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark
| | - Malene Juul
- Bioinformatics Research Centre, Aarhus University, C.F. Mollers Alle 8, Aarhus C, DK-8000, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark
| | - Asger Hobolth
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark
| |
Collapse
|
53
|
Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep 2018; 23:239-254.e6. [PMID: 29617664 PMCID: PMC5961503 DOI: 10.1016/j.celrep.2018.03.076] [Citation(s) in RCA: 696] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.
Collapse
Affiliation(s)
| | - Linghua Wang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, USA; Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | | | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Feng
- TESARO Inc., Waltham, MA 02451, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase Miller
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Haoran Chen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Pora Kim
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Matthew H Bailey
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA 94115, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Denise Wolf
- University of California, San Francisco, San Francisco, CA 94115, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer, Houston, TX 77030, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Raymond J Monnat
- Departments of Pathology & Genome Sciences, University of Washington, Seattle, WA 98195-7705, USA.
| | | | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA; Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
| |
Collapse
|
54
|
Palmigiano A, Santaniello F, Cerutti A, Penkov D, Purushothaman D, Makhija E, Luzi L, di Fagagna FD, Pelicci PG, Shivashankar V, Dellino GI, Blasi F. PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry. Sci Rep 2018; 8:3198. [PMID: 29453404 PMCID: PMC5816642 DOI: 10.1038/s41598-018-21363-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/01/2018] [Indexed: 12/15/2022] Open
Abstract
The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the genome by down-regulating the tumor suppressor PREP1 (PKNOX1). Indeed, DNA combing shows that PREP1 down-regulation affects DNA replication rate, increases the number of simultaneously firing origins and the asymmetry of DNA replication, leading to DNA damage. Genome-wide analysis of replication timing by Repli-seq shows that, upon PREP1 down-regulation, 25% of the genome is replicated earlier in the S-phase. The targeted DNA sequences correspond to Lamin-Associated Domains (LADs), and include late-replicating (LRRs) and temporal transition regions (TTRs). Notably, the distribution of PREP1 DNA binding sites and of its target genes indicates that DNA replication defects are independent of the overall PREP1 transcriptional activity. Finally, PREP1 down-regulation causes a substantial decrease in Lamin B1 levels. This suggests that DNA is released from the nuclear lamina earlier than in the control cells and is available for replication, thus explaining timing defects and DNA damage.This is the first evidence that the replication timing of a specific fraction of the human genome is affected by PREP1 tumor suppressor. This previously unknown function might significantly contribute to the genomic instability observed in human tumors.
Collapse
Affiliation(s)
- Angela Palmigiano
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milan, 20138, Italy
| | - Francesco Santaniello
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
| | - Aurora Cerutti
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Oncogenomics Department, Netherland Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Dmitry Penkov
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Lomonosov Moscow State University, Leninskiye Gori 1, 119991, Moscow, Russia
| | - Divya Purushothaman
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
| | - Ekta Makhija
- Mechano-Biology Institute, National University of Singapore, Singapore, Singapore
| | - Lucilla Luzi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Viveswara Shivashankar
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Mechano-Biology Institute, National University of Singapore, Singapore, Singapore
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy.
| | - Francesco Blasi
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy.
| |
Collapse
|
55
|
Li X, Xu W, Kang W, Wong SH, Wang M, Zhou Y, Fang X, Zhang X, Yang H, Wong CH, To KF, Chan SL, Chan MTV, Sung JJY, Wu WKK, Yu J. Genomic analysis of liver cancer unveils novel driver genes and distinct prognostic features. Theranostics 2018; 8:1740-1751. [PMID: 29556353 PMCID: PMC5858179 DOI: 10.7150/thno.22010] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/12/2017] [Indexed: 01/04/2023] Open
Abstract
Objective: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease with a dismal prognosis. However, driver genes and prognostic markers in HCC remain to be identified. It is hoped that in-depth analysis of HCC genomes in relation to available clinicopathological information will give rise to novel molecular prognostic markers. Methods: We collected genomic data of 1,061 HCC patients from previous studies, and performed integrative analysis to identify significantly mutated genes and molecular prognosticators. We employed three MutSig algorithms (MutSigCV, MutSigCL and MutSigFN) to identify significantly mutated genes. The GISTIC2 algorithm was used to delineate focally amplified and deleted genomic regions. Nonnegative matrix factorization (NMF) was utilized to decipher mutational signatures. Kaplan-Meier survival and Cox regression analyses were used to associate gene mutation and copy number alteration with survival outcome. Logistic regression model was applied to test association between gene mutation and mutational signatures. Results: We discovered 11 novel driver genes, including RNF213, VAV3 and TNRC6B, with mutational prevalence ranging from 1% to 3%. Seven mutational signatures were also identified in HCC, some of which were associated with mutations of classical driver genes (e.g., TP53, TERT) as well as alcohol consumption. Focal amplifications of TERT and other druggable targets, including AURKA, were also revealed. Targeting AURKA by a small-molecule inhibitor potently induced apoptosis in HCC cells. We further demonstrated that HCC patients with TERT amplification displayed shortened overall survival independent of other clinicopathological parameters. In conclusion, our study identified novel cancer driver genes and prognostic markers in HCC, reiterating the translational importance of omics data in the precision medicine era.
Collapse
Affiliation(s)
- Xiangchun Li
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
- Public Laboratory, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Weiqi Xu
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Sunny H Wong
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Mengyao Wang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Yong Zhou
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Xiaodong Fang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Xiuqing Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Huanming Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
- James D. Watson Institute of Genome Sciences, 310058, Hangzhou, People's Republic of China
| | - Chi H Wong
- Department of Clinical Oncology, State Key Laboratory in Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Ka F To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Stephen L Chan
- Department of Clinical Oncology, State Key Laboratory in Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Joseph J Y Sung
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - William K K Wu
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| |
Collapse
|
56
|
Cuppens T, Moisse M, Depreeuw J, Annibali D, Colas E, Gil-Moreno A, Huvila J, Carpén O, Zikán M, Matias-Guiu X, Moerman P, Croce S, Lambrechts D, Amant F. Integrated genome analysis of uterine leiomyosarcoma to identify novel driver genes and targetable pathways. Int J Cancer 2017; 142:1230-1243. [DOI: 10.1002/ijc.31129] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/31/2017] [Accepted: 09/28/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Tine Cuppens
- Department of Oncology, Gynecologic Oncology; KU Leuven (University of Leuven); Leuven 3000 Belgium
- VIB Center for Cancer Biology, VIB; Leuven Belgium
| | - Matthieu Moisse
- Laboratory for Translational Genetics, Department of Human Genetics; KU Leuven; Leuven Belgium
| | - Jeroen Depreeuw
- Department of Oncology, Gynecologic Oncology; KU Leuven (University of Leuven); Leuven 3000 Belgium
- VIB Center for Cancer Biology, VIB; Leuven Belgium
- Laboratory for Translational Genetics, Department of Human Genetics; KU Leuven; Leuven Belgium
| | - Daniela Annibali
- Department of Oncology, Gynecologic Oncology; KU Leuven (University of Leuven); Leuven 3000 Belgium
| | - Eva Colas
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, CIBERONC; Barcelona Spain
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, CIBERONC; Barcelona Spain
- Gynecological Oncology Department; Vall Hebron University Hospital; Barcelona Spain
| | - Jutta Huvila
- Department of Pathology; University of Turku and Turku University Hospital; Turku Finland
| | - Olli Carpén
- Department of Pathology; University of Turku and Turku University Hospital; Turku Finland
- Department of Pathology and Genome Scale Research Program; University of Helsinki and HUSLAB, Helsinki University Hospital; Helsinki Finland
| | - Michal Zikán
- Department of Obstetrics and Gynecology; Gynecological Oncology Center, Charles University in Prague, 1st Faculty of Medicine and General University Hospital in Prague; Prague Czech Republic
| | - Xavier Matias-Guiu
- Pathological Oncology Group and Pathology Department; Hospital U Arnau de Vilanova, and Hospital U de Bellvitge, IRBLLEIDA and Idibell, University of Lleida, CIBERONC; Lleida Spain
| | - Philippe Moerman
- Department of Pathology; UZ Leuven - KU Leuven (University of Leuven); Leuven B-3000 Belgium
| | - Sabrina Croce
- Department of Biopathology; Institut Bergonié; Bordeaux F-33000 France
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB; Leuven Belgium
- Laboratory for Translational Genetics, Department of Human Genetics; KU Leuven; Leuven Belgium
| | - Frédéric Amant
- Department of Oncology, Gynecologic Oncology; KU Leuven (University of Leuven); Leuven 3000 Belgium
- Centre for Gynecologic Oncology Amsterdam (CGOA), Antoni Van Leeuwenhoek - Netherlands Cancer Institute; Amsterdam The Netherlands
| |
Collapse
|
57
|
Wear EE, Song J, Zynda GJ, LeBlanc C, Lee TJ, Mickelson-Young L, Concia L, Mulvaney P, Szymanski ES, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF. Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize ( Zea mays) Root Tips. THE PLANT CELL 2017; 29:2126-2149. [PMID: 28842533 PMCID: PMC5635974 DOI: 10.1105/tpc.17.00037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/31/2017] [Accepted: 08/24/2017] [Indexed: 05/19/2023]
Abstract
All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.
Collapse
Affiliation(s)
- Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Chantal LeBlanc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Lorenzo Concia
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Patrick Mulvaney
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Eric S Szymanski
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - George C Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
58
|
Siefert JC, Georgescu C, Wren JD, Koren A, Sansam CL. DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation. Genome Res 2017; 27:1406-1416. [PMID: 28512193 PMCID: PMC5538556 DOI: 10.1101/gr.218602.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/08/2017] [Indexed: 11/29/2022]
Abstract
In dividing cells, DNA replication occurs in a precise order, but many questions remain regarding the mechanisms of replication timing establishment and regulation. We now have generated genome-wide, high-resolution replication timing maps throughout zebrafish development. Unexpectedly, in the rapid cell cycles preceding the midblastula transition, a defined timing program was present that predicted the initial wave of zygotic transcription. Replication timing was thereafter progressively and continuously remodeled across the majority of the genome, and epigenetic changes involved in enhancer activation frequently paralleled developmental changes in replication timing. The long arm of Chromosome 4 underwent a dramatic developmentally regulated switch to late replication during gastrulation, reminiscent of mammalian X Chromosome inactivation. This study reveals that replication timing is dynamic and tightly linked to epigenetic and transcriptional changes throughout early zebrafish development. These data provide insight into the regulation and functions of replication timing and will enable further mechanistic studies.
Collapse
Affiliation(s)
- Joseph C Siefert
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Constantin Georgescu
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Christopher L Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| |
Collapse
|
59
|
Blumenfeld B, Ben-Zimra M, Simon I. Perturbations in the Replication Program Contribute to Genomic Instability in Cancer. Int J Mol Sci 2017; 18:E1138. [PMID: 28587102 PMCID: PMC5485962 DOI: 10.3390/ijms18061138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 12/14/2022] Open
Abstract
Cancer and genomic instability are highly impacted by the deoxyribonucleic acid (DNA) replication program. Inaccuracies in DNA replication lead to the increased acquisition of mutations and structural variations. These inaccuracies mainly stem from loss of DNA fidelity due to replication stress or due to aberrations in the temporal organization of the replication process. Here we review the mechanisms and impact of these major sources of error to the replication program.
Collapse
Affiliation(s)
- Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Micha Ben-Zimra
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
- Pharmacology and Experimental Therapeutics Unit, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| |
Collapse
|
60
|
Reinhart M, Cardoso MC. A journey through the microscopic ages of DNA replication. PROTOPLASMA 2017; 254:1151-1162. [PMID: 27943022 PMCID: PMC5376393 DOI: 10.1007/s00709-016-1058-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
Scientific discoveries and technological advancements are inseparable but not always take place in a coherent chronological manner. In the next, we will provide a seemingly unconnected and serendipitous series of scientific facts that, in the whole, converged to unveil DNA and its duplication. We will not cover here the many and fundamental contributions from microbial genetics and in vitro biochemistry. Rather, in this journey, we will emphasize the interplay between microscopy development culminating on super resolution fluorescence microscopy (i.e., nanoscopy) and digital image analysis and its impact on our understanding of DNA duplication. We will interlace the journey with landmark concepts and experiments that have brought the cellular DNA replication field to its present state.
Collapse
Affiliation(s)
- Marius Reinhart
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.
| |
Collapse
|
61
|
Juul M, Bertl J, Guo Q, Nielsen MM, Świtnicki M, Hornshøj H, Madsen T, Hobolth A, Pedersen JS. Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate. eLife 2017; 6. [PMID: 28362259 PMCID: PMC5440169 DOI: 10.7554/elife.21778] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5'UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance.
Collapse
Affiliation(s)
- Malene Juul
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Johanna Bertl
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Qianyun Guo
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Michał Świtnicki
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Tobias Madsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Asger Hobolth
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| |
Collapse
|
62
|
Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features. Sci Rep 2017; 7:41544. [PMID: 28128360 PMCID: PMC5269722 DOI: 10.1038/srep41544] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/22/2016] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold missing drivers of tumourigenesis, but few such "driver lncRNAs" are known. Until now, they have been discovered through changes in expression, leading to problems in distinguishing between causative roles and passenger effects. We here present a different approach for driver lncRNA discovery using mutational patterns in tumour DNA. Our pipeline, ExInAtor, identifies genes with excess load of somatic single nucleotide variants (SNVs) across panels of tumour genomes. Heterogeneity in mutational signatures between cancer types and individuals is accounted for using a simple local trinucleotide background model, which yields high precision and low computational demands. We use ExInAtor to predict drivers from the GENCODE annotation across 1112 entire genomes from 23 cancer types. Using a stratified approach, we identify 15 high-confidence candidates: 9 novel and 6 known cancer-related genes, including MALAT1, NEAT1 and SAMMSON. Both known and novel driver lncRNAs are distinguished by elevated gene length, evolutionary conservation and expression. We have presented a first catalogue of mutated lncRNA genes driving cancer, which will grow and improve with the application of ExInAtor to future tumour genome projects.
Collapse
|
63
|
Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol 2016; 17:241. [PMID: 27894357 PMCID: PMC5125044 DOI: 10.1186/s13059-016-1110-1] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.
Collapse
Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Alexander Hoischen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| |
Collapse
|
64
|
Pfeifer SP, Jensen JD. The Impact of Linked Selection in Chimpanzees: A Comparative Study. Genome Biol Evol 2016; 8:3202-3208. [PMID: 27678122 PMCID: PMC5174744 DOI: 10.1093/gbe/evw240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the relative importance of these forces is the common observation of a strong positive correlation between nucleotide diversity and recombination rate. While indeed observed in humans, the interpretation of this pattern has been difficult in the absence of high-quality polymorphism data and recombination maps in closely related species. Here, we characterize genetic features driving nucleotide diversity in Western chimpanzees using a recently generated whole genome polymorphism data set. Our results suggest that recombination rate is the primary predictor of nucleotide variation with a strongly positive correlation. In addition, telomeric distance, regional GC-content, and regional CpG-island content are strongly negatively correlated with variation. These results are compared with humans, with both similarities and differences interpreted in the light of the estimated effective population sizes of the two species as well as their strongly differing recent demographic histories.
Collapse
Affiliation(s)
- Susanne P Pfeifer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,School of Life Sciences, Arizona State University (ASU), Tempe, Arizona
| | - Jeffrey D Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,School of Life Sciences, Arizona State University (ASU), Tempe, Arizona
| |
Collapse
|
65
|
Callegari AJ, Kelly TJ. Coordination of DNA damage tolerance mechanisms with cell cycle progression in fission yeast. Cell Cycle 2016; 15:261-73. [PMID: 26652183 PMCID: PMC5007584 DOI: 10.1080/15384101.2015.1121353] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA damage tolerance (DDT) mechanisms allow cells to synthesize a new DNA strand when the template is damaged. Many mutations resulting from DNA damage in eukaryotes are generated during DDT when cells use the mutagenic translesion polymerases, Rev1 and Polζ, rather than mechanisms with higher fidelity. The coordination among DDT mechanisms is not well understood. We used live-cell imaging to study the function of DDT mechanisms throughout the cell cycle of the fission yeast Schizosaccharomyces pombe. We report that checkpoint-dependent mitotic delay provides a cellular mechanism to ensure the completion of high fidelity DDT, largely by homology-directed repair (HDR). DDT by mutagenic polymerases is suppressed during the checkpoint delay by a mechanism dependent on Rad51 recombinase. When cells pass the G2/M checkpoint and can no longer delay mitosis, they completely lose the capacity for HDR and simultaneously exhibit a requirement for Rev1 and Polζ. Thus, DDT is coordinated with the checkpoint response so that the activity of mutagenic polymerases is confined to a vulnerable period of the cell cycle when checkpoint delay and HDR are not possible.
Collapse
Affiliation(s)
- A John Callegari
- a Molecular Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| | - Thomas J Kelly
- a Molecular Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| |
Collapse
|
66
|
Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS. Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri. Mol Biol Evol 2016; 34:93-109. [PMID: 27744412 PMCID: PMC5854121 DOI: 10.1093/molbev/msw224] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-%GC squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10-3/genome/generation. Vibrio fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.
Collapse
Affiliation(s)
- Marcus M Dillon
- Microbiology Graduate Program, University of New Hampshire, Durham, NH
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, NC.,Department of Biology, Indiana University, Bloomington, IN
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
| | - Vaughn S Cooper
- Microbiology Graduate Program, University of New Hampshire, Durham, NH .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| |
Collapse
|
67
|
Kaiser VB, Taylor MS, Semple CA. Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types. PLoS Genet 2016; 12:e1006207. [PMID: 27490693 PMCID: PMC4973979 DOI: 10.1371/journal.pgen.1006207] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 06/29/2016] [Indexed: 02/07/2023] Open
Abstract
Disruption of gene regulation is known to play major roles in carcinogenesis and tumour progression. Here, we comprehensively characterize the mutational profiles of diverse transcription factor binding sites (TFBSs) across 1,574 completely sequenced cancer genomes encompassing 11 tumour types. We assess the relative rates and impact of the mutational burden at the binding sites of 81 transcription factors (TFs), by comparing the abundance and patterns of single base substitutions within putatively functional binding sites to control sites with matched sequence composition. There is a strong (1.43-fold) and significant excess of mutations at functional binding sites across TFs, and the mutations that accumulate in cancers are typically more disruptive than variants tolerated in extant human populations at the same sites. CTCF binding sites suffer an exceptionally high mutational load in cancer (3.31-fold excess) relative to control sites, and we demonstrate for the first time that this effect is seen in essentially all cancer types with sufficient data. The sub-set of CTCF sites involved in higher order chromatin structures has the highest mutational burden, suggesting a widespread breakdown of chromatin organization. However, we find no evidence for selection driving these distinctive patterns of mutation. The mutational load at CTCF-binding sites is substantially determined by replication timing and the mutational signature of the tumor in question, suggesting that selectively neutral processes underlie the unusual mutation patterns. Pervasive hyper-mutation within transcription factor binding sites rewires the regulatory landscape of the cancer genome, but it is dominated by mutational processes rather than selection. Regulatory regions of the genome are important players in cancer initiation and progression. Here, we study the patterns of mutations accumulating at short DNA segments bound by regulatory proteins (transcription factor binding sites) across many cancer types and in the human population. We find strikingly high rates of mutation at active regulatory sites across different cancers, relative to matched control sequences. This excess of mutations disrupts the binding sites of particular factors, such as CTCF, and is likely to be driven by selectively neutral processes, such as the replication timing of the genomic regions concerned. However, binding sites involved in regulatory chromatin structures suffer particularly high levels of mutation, suggesting the frequent disruption of such structures in cancers.
Collapse
Affiliation(s)
- Vera B Kaiser
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| |
Collapse
|
68
|
Drillon G, Audit B, Argoul F, Arneodo A. Evidence of selection for an accessible nucleosomal array in human. BMC Genomics 2016; 17:526. [PMID: 27472913 PMCID: PMC4966569 DOI: 10.1186/s12864-016-2880-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/04/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Recently, a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix has been used to reveal some enrichment of nucleosome-inhibiting energy barriers (NIEBs) nearby ubiquitous human "master" replication origins. Here we use this model to predict the existence of about 1.6 millions NIEBs over the 22 human autosomes. RESULTS We show that these high energy barriers of mean size 153 bp correspond to nucleosome-depleted regions (NDRs) in vitro, as expected, but also in vivo. On either side of these NIEBs, we observe, in vivo and in vitro, a similar compacted nucleosome ordering, suggesting an absence of chromatin remodeling. This nucleosomal ordering strongly correlates with oscillations of the GC content as well as with the interspecies and intraspecies mutation profiles along these regions. Comparison of these divergence rates reveals the existence of both positive and negative selections linked to nucleosome positioning around these intrinsic NDRs. Overall, these NIEBs and neighboring nucleosomes cover 37.5 % of the human genome where nucleosome occupancy is stably encoded in the DNA sequence. These 1 kb-sized regions of intrinsic nucleosome positioning are equally found in GC-rich and GC-poor isochores, in early and late replicating regions, in intergenic and genic regions but not at gene promoters. CONCLUSION The source of selection pressure on the NIEBs has yet to be resolved in future work. One possible scenario is that these widely distributed chromatin patterns have been selected in human to impair the condensation of the nucleosomal array into the 30 nm chromatin fiber, so as to facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner.
Collapse
Affiliation(s)
- Guénola Drillon
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Benjamin Audit
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Françoise Argoul
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
| | - Alain Arneodo
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
| |
Collapse
|
69
|
Kenigsberg E, Yehuda Y, Marjavaara L, Keszthelyi A, Chabes A, Tanay A, Simon I. The mutation spectrum in genomic late replication domains shapes mammalian GC content. Nucleic Acids Res 2016; 44:4222-32. [PMID: 27085808 PMCID: PMC4872117 DOI: 10.1093/nar/gkw268] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/10/2016] [Accepted: 03/30/2016] [Indexed: 11/14/2022] Open
Abstract
Genome sequence compositions and epigenetic organizations are correlated extensively across multiple length scales. Replication dynamics, in particular, is highly correlated with GC content. We combine genome-wide time of replication (ToR) data, topological domains maps and detailed functional epigenetic annotations to study the correlations between replication timing and GC content at multiple scales. We find that the decrease in genomic GC content at large scale late replicating regions can be explained by mutation bias favoring A/T nucleotide, without selection or biased gene conversion. Quantification of the free dNTP pool during the cell cycle is consistent with a mechanism involving replication-coupled mutation spectrum that favors AT nucleotides at late S-phase. We suggest that mammalian GC content composition is shaped by independent forces, globally modulating mutation bias and locally selecting on functional element. Deconvoluting these forces and analyzing them on their native scales is important for proper characterization of complex genomic correlations.
Collapse
Affiliation(s)
- Ephraim Kenigsberg
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Yehuda
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lisette Marjavaara
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Andrea Keszthelyi
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
70
|
The tandem duplicator phenotype as a distinct genomic configuration in cancer. Proc Natl Acad Sci U S A 2016; 113:E2373-82. [PMID: 27071093 DOI: 10.1073/pnas.1520010113] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing studies have revealed genome-wide structural variation patterns in cancer, such as chromothripsis and chromoplexy, that do not engage a single discernable driver mutation, and whose clinical relevance is unclear. We devised a robust genomic metric able to identify cancers with a chromotype called tandem duplicator phenotype (TDP) characterized by frequent and distributed tandem duplications (TDs). Enriched only in triple-negative breast cancer (TNBC) and in ovarian, endometrial, and liver cancers, TDP tumors conjointly exhibit tumor protein p53 (TP53) mutations, disruption of breast cancer 1 (BRCA1), and increased expression of DNA replication genes pointing at rereplication in a defective checkpoint environment as a plausible causal mechanism. The resultant TDs in TDP augment global oncogene expression and disrupt tumor suppressor genes. Importantly, the TDP strongly correlates with cisplatin sensitivity in both TNBC cell lines and primary patient-derived xenografts. We conclude that the TDP is a common cancer chromotype that coordinately alters oncogene/tumor suppressor expression with potential as a marker for chemotherapeutic response.
Collapse
|
71
|
Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy VB, Sharpe HJ, McKee T, Letourneau A, Ribaux PG, Popadin K, Basset-Seguin N, Ben Chaabene R, Santoni FA, Andrianova MA, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage FJ, Antonarakis SE, Nikolaev SI. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma. Nat Genet 2016; 48:398-406. [PMID: 26950094 DOI: 10.1038/ng.3525] [Citation(s) in RCA: 326] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/11/2016] [Indexed: 12/13/2022]
Abstract
Basal cell carcinoma (BCC) of the skin is the most common malignant neoplasm in humans. BCC is primarily driven by the Sonic Hedgehog (Hh) pathway. However, its phenotypic variation remains unexplained. Our genetic profiling of 293 BCCs found the highest mutation rate in cancer (65 mutations/Mb). Eighty-five percent of the BCCs harbored mutations in Hh pathway genes (PTCH1, 73% or SMO, 20% (P = 6.6 × 10(-8)) and SUFU, 8%) and in TP53 (61%). However, 85% of the BCCs also harbored additional driver mutations in other cancer-related genes. We observed recurrent mutations in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), and NRAS, KRAS or HRAS (2%), and loss-of-function and deleterious missense mutations were present in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). Consistent with the mutational profiles, N-Myc and Hippo-YAP pathway target genes were upregulated. Functional analysis of the mutations in MYCN, PTPN14 and LATS1 suggested their potential relevance in BCC tumorigenesis.
Collapse
Affiliation(s)
- Ximena Bonilla
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - Bryan King
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Fedor Bezrukov
- Department of Physics, University of Connecticut, Storrs, Connecticut, USA
- RIKEN BNL Research Center, Brookhaven National Laboratory, Upton, New York, USA
| | - Gürkan Kaya
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Hayley J Sharpe
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, California, USA
| | - Thomas McKee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Pascale G Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Konstantin Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Nicole Basset-Seguin
- Department of Dermatology, Saint Louis Hospital, Paris 7 University, Paris, France
| | - Rouaa Ben Chaabene
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Maria A Andrianova
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Michel Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Marco Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Carole Verdan
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Kerstin Grosdemange
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - Olga Sumara
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Oncology, University of Lausanne and Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Frederic J de Sauvage
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, California, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| |
Collapse
|
72
|
Panchin AY, Makeev VJ, Medvedeva YA. Preservation of methylated CpG dinucleotides in human CpG islands. Biol Direct 2016; 11:11. [PMID: 27005429 PMCID: PMC4804638 DOI: 10.1186/s13062-016-0113-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 03/14/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cytosine methylation in the CpG context. Meanwhile the CpG content in genomic regions called CpG islands (CGIs) is noticeably higher. This observation is usually explained by lower CpG > TpG substitution rates within CGIs due to reduced cytosine methylation levels. RESULTS By combining genome-wide data on substitutions and methylation levels in several human cell types we have shown that cytosine methylation in human sperm cells was strongly and consistently associated with increased CpG > TpG substitution rates. In contrast, this correlation was not observed for embryonic stem cells or fibroblasts. Surprisingly, the decreased sperm CpG methylation level was insufficient to explain the reduced CpG > TpG substitution rates in CGIs. CONCLUSIONS While cytosine methylation in human sperm cells is strongly associated with increased CpG > TpG substitution rates, substitution rates are significantly reduced within CGIs even after sperm CpG methylation levels and local GC content are controlled for. Our findings are consistent with strong negative selection preserving methylated CpGs within CGIs including intergenic ones.
Collapse
Affiliation(s)
- Alexander Y Panchin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, GSP-1, 119991, Russia.,Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia.,Moscow Institute of Physics and Technology, Moscow Regoin, 141700, Russia
| | - Yulia A Medvedeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, GSP-1, 119991, Russia. .,Center for Bioengineering, Research Center of Biotechnology RAS, Russian Academy of Science, Moscow, 117312, Russia.
| |
Collapse
|
73
|
Zhang CZ, Pellman D. From Mutational Mechanisms in Single Cells to Mutational Patterns in Cancer Genomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:117-37. [PMID: 26968629 DOI: 10.1101/sqb.2015.80.027623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Analysis of mutations in thousands of cancer genomes has revealed many characteristic patterns of mutagenesis. The search for the molecular mechanisms underlying these mutational patterns has not only generated novel biological insight but also led to the development of new experimental strategies to study cell-to-cell variation and genome evolution. In this essay, we discuss recent progress in the study of mutational mechanisms with a particular emphasis on the analysis of mutagenesis at the single-cell level.
Collapse
Affiliation(s)
- Cheng-Zhong Zhang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142 Howard Hughes Medical Institute, Boston, Massachusetts 02115
| |
Collapse
|
74
|
Petryk N, Kahli M, d'Aubenton-Carafa Y, Jaszczyszyn Y, Shen Y, Silvain M, Thermes C, Chen CL, Hyrien O. Replication landscape of the human genome. Nat Commun 2016; 7:10208. [PMID: 26751768 PMCID: PMC4729899 DOI: 10.1038/ncomms10208] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 11/13/2015] [Indexed: 12/21/2022] Open
Abstract
Despite intense investigation, human replication origins and termini remain elusive. Existing data have shown strong discrepancies. Here we sequenced highly purified Okazaki fragments from two cell types and, for the first time, quantitated replication fork directionality and delineated initiation and termination zones genome-wide. Replication initiates stochastically, primarily within non-transcribed, broad (up to 150 kb) zones that often abut transcribed genes, and terminates dispersively between them. Replication fork progression is significantly co-oriented with the transcription. Initiation and termination zones are frequently contiguous, sometimes separated by regions of unidirectional replication. Initiation zones are enriched in open chromatin and enhancer marks, even when not flanked by genes, and often border ‘topologically associating domains' (TADs). Initiation zones are enriched in origin recognition complex (ORC)-binding sites and better align to origins previously mapped using bubble-trap than λ-exonuclease. This novel panorama of replication reveals how chromatin and transcription modulate the initiation process to create cell-type-specific replication programs. The physical origin and termination sites of DNA replication in human cells have remained elusive. Here the authors use Okazaki fragment sequencing to reveal global replication patterns and show how chromatin and transcription modulate the process.
Collapse
Affiliation(s)
- Nataliya Petryk
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, 46 rue d'Ulm, Paris F-75005, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Malik Kahli
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, 46 rue d'Ulm, Paris F-75005, France
| | - Yves d'Aubenton-Carafa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Yimin Shen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Maud Silvain
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Claude Thermes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Chun-Long Chen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Olivier Hyrien
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, 46 rue d'Ulm, Paris F-75005, France
| |
Collapse
|
75
|
Abstract
A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in gene regulation rather than differences at the protein level. Over the past few years, evolutionary studies have shifted from mere sequence comparisons to integrative analyses in which gene regulation is key to understanding species evolution. DNA methylation is an important epigenetic modification involved in the regulation of numerous biological processes. Nevertheless, the evolution of the human methylome and the processes driving such changes are poorly understood. Here, we review the close interplay between Cytosine-phosphate-Guanine (CpG) methylation and the underlying genome sequence, as well as its evolutionary impact. We also summarize the latest advances in the field, revisiting the main literature on human and nonhuman primates. We hope to encourage the scientific community to address the many challenges posed by the field of comparative epigenomics.
Collapse
|
76
|
Leibowitz ML, Zhang CZ, Pellman D. Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annu Rev Genet 2015; 49:183-211. [DOI: 10.1146/annurev-genet-120213-092228] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mitchell L. Leibowitz
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
| | - Cheng-Zhong Zhang
- Department of Pediatric Oncology,
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - David Pellman
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
| |
Collapse
|
77
|
Price N, Graur D. Are Synonymous Sites in Primates and Rodents Functionally Constrained? J Mol Evol 2015; 82:51-64. [PMID: 26563252 DOI: 10.1007/s00239-015-9719-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 11/04/2015] [Indexed: 11/28/2022]
Abstract
It has been claimed that synonymous sites in mammals are under selective constraint. Furthermore, in many studies the selective constraint at such sites in primates was claimed to be more stringent than that in rodents. Given the larger effective population sizes in rodents than in primates, the theoretical expectation is that selection in rodents would be more effective than that in primates. To resolve this contradiction between expectations and observations, we used processed pseudogenes as a model for strict neutral evolution, and estimated selective constraint on synonymous sites using the rate of substitution at pseudosynonymous and pseudononsynonymous sites in pseudogenes as the neutral expectation. After controlling for the effects of GC content, our results were similar to those from previous studies, i.e., synonymous sites in primates exhibited evidence for higher selective constraint that those in rodents. Specifically, our results indicated that in primates up to 24% of synonymous sites could be under purifying selection, while in rodents synonymous sites evolved neutrally. To further control for shifts in GC content, we estimated selective constraint at fourfold degenerate sites using a maximum parsimony approach. This allowed us to estimate selective constraint using mutational patterns that cause a shift in GC content (GT ↔ TG, CT ↔ TC, GA ↔ AG, and CA ↔ AC) and ones that do not (AT ↔ TA and CG ↔ GC). Using this approach, we found that synonymous sites evolve neutrally in both primates and rodents. Apparent deviations from neutrality were caused by a higher rate of C → A and C → T mutations in pseudogenes. Such differences are most likely caused by the shift in GC content experienced by pseudogenes. We conclude that previous estimates according to which 20-40% of synonymous sites in primates were under selective constraint were most likely artifacts of the biased pattern of mutation.
Collapse
Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Dan Graur
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| |
Collapse
|
78
|
Darcy DG, Chiaroni-Clarke R, Murphy JM, Honeyman JN, Bhanot U, LaQuaglia MP, Simon SM. The genomic landscape of fibrolamellar hepatocellular carcinoma: whole genome sequencing of ten patients. Oncotarget 2015; 6:755-70. [PMID: 25605237 PMCID: PMC4359253 DOI: 10.18632/oncotarget.2712] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/11/2014] [Indexed: 12/13/2022] Open
Abstract
Fibrolamellar hepatocellular carcinoma is a rare, malignant liver tumor that often arises in the otherwise normal liver of adolescents and young adults. Previous studies have focused on biomarkers and comparisons to traditional hepatocellular carcinoma, and have yielded little data on the underlying pathophysiology. We performed whole genome sequencing on paired tumor and normal samples from 10 patients to identify recurrent mutations and structural variations that could predispose to oncogenesis. There are relatively few coding, somatic mutations in this cancer, putting it on the low end of the mutational spectrum. Aside from a previously described heterozygous deletion on chromosome 19 that encodes for a functional, chimeric protein, there were no other recurrent structural variations that contribute to the tumor genotype. The lack of a second-hit mutation in the genomic landscape of fibrolamellar hepatocellular carcinoma makes the DNAJB1-PRKACA fusion protein the best target for diagnostic and therapeutic advancements. The mutations, altered pathways and structural variants that characterized fibrolamellar hepatocellular carcinoma were distinct from those in hepatocellular carcinoma, further defining it as a distinct carcinoma.
Collapse
Affiliation(s)
- David G Darcy
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA.,Division of Pediatric Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Jennifer M Murphy
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA.,Division of Pediatric Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joshua N Honeyman
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA.,Division of Pediatric Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Umesh Bhanot
- Pathology Core, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael P LaQuaglia
- Division of Pediatric Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA
| |
Collapse
|
79
|
Seplyarskiy VB, Bazykin GA, Soldatov RA. Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures. Mol Biol Evol 2015; 32:3158-72. [PMID: 26376651 DOI: 10.1093/molbev/msv184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Replication timing is an important determinant of germline mutation patterns, with a higher rate of point mutations in late replicating regions. Mechanisms underlying this association remain elusive. One of the suggested explanations is the activity of error-prone DNA polymerases in late-replicating regions. Polymerase zeta (pol ζ), an essential error-prone polymerase biased toward transversions, also has a tendency to produce dinucleotide mutations (DNMs), complex mutational events that simultaneously affect two adjacent nucleotides. Experimental studies have shown that pol ζ is strongly biased toward GC→AA/TT DNMs. Using primate divergence data, we show that the GC→AA/TT pol ζ mutational signature is the most frequent among DNMs, and its rate exceeds the mean rate of other DNM types by a factor of approximately 10. Unlike the overall rate of DNMs, the pol ζ signature drastically increases with the replication time in the human genome. Finally, the pol ζ signature is enriched in transcribed regions, and there is a strong prevalence of GC→TT over GC→AA DNMs on the nontemplate strand, indicating association with transcription. A recurrently occurring GC→TT DNM in HRAS and SOD1 genes causes the Costello syndrome and amyotrophic lateral sclerosis correspondently; we observe an approximately 1 kb long mutation hotspot enriched by transversions near these DNMs in both cases, suggesting a link between these diseases and pol ζ activity. This study uncovers the genomic preferences of pol ζ, shedding light on a novel cause of mutational heterogeneity along the genome.
Collapse
Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Georgii A Bazykin
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
80
|
Meryet-Figuiere M, Alaei-Mahabadi B, Ali MM, Mitra S, Subhash S, Pandey GK, Larsson E, Kanduri C. Temporal separation of replication and transcription during S-phase progression. Cell Cycle 2015; 13:3241-8. [PMID: 25485504 DOI: 10.4161/15384101.2014.953876] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcriptional events during S-phase are critical for cell cycle progression. Here, by using a nascent RNA capture assay coupled with high-throughput sequencing, we determined the temporal patterns of transcriptional events that occur during S-phase. We show that genes involved in critical S-phase-specific biological processes such as nucleosome assembly and DNA repair have temporal transcription patterns across S-phase that are not evident from total RNA levels. By comparing transcription timing with replication timing in S-phase, we show that early replicating genes show increased transcription late in S-phase whereas late replicating genes are predominantly transcribed early in S-phase. Global anti-correlation between replication and transcription timing was observed only based on nascent RNA but not total RNA. Our data provides a detailed view of ongoing transcriptional events during the S-phase of cell cycle, and supports that transcription and replication are temporally separated.
Collapse
Affiliation(s)
- Matthieu Meryet-Figuiere
- a Department of Medical Genetics; Institute of Biomedicine; The Sahlgrenska Academy ; University of Gothenburg ; Gothenburg , Sweden
| | | | | | | | | | | | | | | |
Collapse
|
81
|
Katainen R, Dave K, Pitkänen E, Palin K, Kivioja T, Välimäki N, Gylfe AE, Ristolainen H, Hänninen UA, Cajuso T, Kondelin J, Tanskanen T, Mecklin JP, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Kaasinen E, Kilpivaara O, Tuupanen S, Enge M, Taipale J, Aaltonen LA. CTCF/cohesin-binding sites are frequently mutated in cancer. Nat Genet 2015; 47:818-21. [PMID: 26053496 DOI: 10.1038/ng.3335] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/12/2015] [Indexed: 12/12/2022]
Abstract
Cohesin is present in almost all active enhancer regions, where it is associated with transcription factors. Cohesin frequently colocalizes with CTCF (CCCTC-binding factor), affecting genomic stability, expression and epigenetic homeostasis. Cohesin subunits are mutated in cancer, but CTCF/cohesin-binding sites (CBSs) in DNA have not been examined for mutations. Here we report frequent mutations at CBSs in cancers displaying a mutational signature where mutations in A•T base pairs predominate. Integration of whole-genome sequencing data from 213 colorectal cancer (CRC) samples and chromatin immunoprecipitation sequencing (ChIP-exo) data identified frequent point mutations at CBSs. In contrast, CRCs showing an ultramutator phenotype caused by defects in the exonuclease domain of DNA polymerase ɛ (POLE) displayed significantly fewer mutations at and adjacent to CBSs. Analysis of public data showed that multiple cancer types accumulate CBS mutations. CBSs are a major mutational hotspot in the noncoding cancer genome.
Collapse
Affiliation(s)
- Riku Katainen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Kashyap Dave
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Esa Pitkänen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Teemu Kivioja
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Alexandra E Gylfe
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Heikki Ristolainen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Ulrika A Hänninen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Tatiana Cajuso
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland
| | - Heikki Järvinen
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Eevi Kaasinen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Outi Kilpivaara
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Sari Tuupanen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Martin Enge
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Jussi Taipale
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Lauri A Aaltonen
- 1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| |
Collapse
|
82
|
The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia. Genetics 2015; 200:935-46. [PMID: 25971664 DOI: 10.1534/genetics.115.176834] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/07/2015] [Indexed: 12/18/2022] Open
Abstract
Spontaneous mutations are ultimately essential for evolutionary change and are also the root cause of many diseases. However, until recently, both biological and technical barriers have prevented detailed analyses of mutation profiles, constraining our understanding of the mutation process to a few model organisms and leaving major gaps in our understanding of the role of genome content and structure on mutation. Here, we present a genome-wide view of the molecular mutation spectrum in Burkholderia cenocepacia, a clinically relevant pathogen with high %GC content and multiple chromosomes. We find that B. cenocepacia has low genome-wide mutation rates with insertion-deletion mutations biased toward deletions, consistent with the idea that deletion pressure reduces prokaryotic genome sizes. Unlike prior studies of other organisms, mutations in B. cenocepacia are not AT biased, which suggests that at least some genomes with high %GC content experience unusual base-substitution mutation pressure. Importantly, we also observe variation in both the rates and spectra of mutations among chromosomes and elevated G:C > T:A transversions in late-replicating regions. Thus, although some patterns of mutation appear to be highly conserved across cellular life, others vary between species and even between chromosomes of the same species, potentially influencing the evolution of nucleotide composition and genome architecture.
Collapse
|
83
|
Boulos RE, Drillon G, Argoul F, Arneodo A, Audit B. Structural organization of human replication timing domains. FEBS Lett 2015; 589:2944-57. [PMID: 25912651 DOI: 10.1016/j.febslet.2015.04.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 12/16/2022]
Abstract
Recent analysis of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided increasing evidence that flexibility in replication origin usage is regulated locally by the epigenetic landscape and over larger genomic distances by the 3D chromatin architecture. Here, we review the recent results establishing some link between replication domains and chromatin structural domains in pluripotent and various differentiated cell types in human. We reconcile the originally proposed dichotomic picture of early and late constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the U-shaped MRT domains bordered by "master" replication origins specified by a localized (∼200-300 kb) zone of open and transcriptionally active chromatin from which a replication wave likely initiates and propagates toward the domain center via a cascade of origin firing. We discuss the relationships between these MRT domains, topologically associated domains and lamina-associated domains. This review sheds a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and the determination of differentiation properties.
Collapse
Affiliation(s)
- Rasha E Boulos
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Guénola Drillon
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Françoise Argoul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Alain Arneodo
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Benjamin Audit
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.
| |
Collapse
|
84
|
Grove CS, Vassiliou GS. Acute myeloid leukaemia: a paradigm for the clonal evolution of cancer? Dis Model Mech 2015; 7:941-51. [PMID: 25056697 PMCID: PMC4107323 DOI: 10.1242/dmm.015974] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acute myeloid leukaemia (AML) is an uncontrolled clonal proliferation of abnormal myeloid progenitor cells in the bone marrow and blood. Advances in cancer genomics have revealed the spectrum of somatic mutations that give rise to human AML and drawn our attention to its molecular evolution and clonal architecture. It is now evident that most AML genomes harbour small numbers of mutations, which are acquired in a stepwise manner. This characteristic, combined with our ability to identify mutations in individual leukaemic cells and our detailed understanding of normal human and murine haematopoiesis, makes AML an excellent model for understanding the principles of cancer evolution. Furthermore, a better understanding of how AML evolves can help us devise strategies to improve the therapy and prognosis of AML patients. Here, we draw from recent advances in genomics, clinical studies and experimental models to describe the current knowledge of the clonal evolution of AML and its implications for the biology and treatment of leukaemias and other cancers.
Collapse
Affiliation(s)
- Carolyn S Grove
- Haematological Cancer Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| |
Collapse
|
85
|
Chen L, Shern JF, Wei JS, Yohe ME, Song YK, Hurd L, Liao H, Catchpoole D, Skapek SX, Barr FG, Hawkins DS, Khan J. Clonality and evolutionary history of rhabdomyosarcoma. PLoS Genet 2015; 11:e1005075. [PMID: 25768946 PMCID: PMC4358975 DOI: 10.1371/journal.pgen.1005075] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/16/2015] [Indexed: 01/06/2023] Open
Abstract
To infer the subclonality of rhabdomyosarcoma (RMS) and predict the temporal order of genetic events for the tumorigenic process, and to identify novel drivers, we applied a systematic method that takes into account germline and somatic alterations in 44 tumor-normal RMS pairs using deep whole-genome sequencing. Intriguingly, we find that loss of heterozygosity of 11p15.5 and mutations in RAS pathway genes occur early in the evolutionary history of the PAX-fusion-negative-RMS (PFN-RMS) subtype. We discover several early mutations in non-RAS mutated samples and predict them to be drivers in PFN-RMS including recurrent mutation of PKN1. In contrast, we find that PAX-fusion-positive (PFP) subtype tumors have undergone whole-genome duplication in the late stage of cancer evolutionary history and have acquired fewer mutations and subclones than PFN-RMS. Moreover we predict that the PAX3-FOXO1 fusion event occurs earlier than the whole genome duplication. Our findings provide information critical to the understanding of tumorigenesis of RMS.
Collapse
Affiliation(s)
- Li Chen
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jack F. Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jun S. Wei
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marielle E. Yohe
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Young K. Song
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Laura Hurd
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hongling Liao
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Catchpoole
- Biospecimens Research and Tumour Bank, The Kids Research Institute, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Stephen X. Skapek
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Frederic G. Barr
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Douglas S. Hawkins
- Department of Pediatrics, Seattle Children’s Hospital, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
86
|
Urban JM, Foulk MS, Casella C, Gerbi SA. The hunt for origins of DNA replication in multicellular eukaryotes. F1000PRIME REPORTS 2015; 7:30. [PMID: 25926981 PMCID: PMC4371235 DOI: 10.12703/p7-30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed.
Collapse
Affiliation(s)
- John M. Urban
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| | - Michael S. Foulk
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Department of Biology, Mercyhurst University501 East 38th Street, Erie, PA 16546USA
| | - Cinzia Casella
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Institute for Molecular Medicine, University of Southern DenmarkJB Winsloews Vej 25, 5000 Odense CDenmark
| | - Susan A. Gerbi
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| |
Collapse
|
87
|
Supek F, Lehner B. Differential DNA mismatch repair underlies mutation rate variation across the human genome. Nature 2015; 521:81-4. [PMID: 25707793 PMCID: PMC4425546 DOI: 10.1038/nature14173] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/19/2014] [Indexed: 12/26/2022]
Abstract
Cancer genome sequencing has revealed considerable variation in somatic mutation rates across the human genome, with mutation rates elevated in heterochromatic late replicating regions and reduced in early replicating euchromatin. Multiple mechanisms have been suggested to underlie this, but the actual cause is unknown. Here we identify variable DNA mismatch repair (MMR) as the basis of this variation. Analysing ∼17 million single-nucleotide variants from the genomes of 652 tumours, we show that regional autosomal mutation rates at megabase resolution are largely stable across cancer types, with differences related to changes in replication timing and gene expression. However, mutations arising after the inactivation of MMR are no longer enriched in late replicating heterochromatin relative to early replicating euchromatin. Thus, differential DNA repair and not differential mutation supply is the primary cause of the large-scale regional mutation rate variation across the human genome.
Collapse
Affiliation(s)
- Fran Supek
- 1] EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain [3] Division of Electronics, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
| | - Ben Lehner
- 1] EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
88
|
Drillon G, Audit B, Argoul F, Arneodo A. Ubiquitous human 'master' origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064102. [PMID: 25563930 DOI: 10.1088/0953-8984/27/6/064102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
As the elementary building block of eukaryotic chromatin, the nucleosome is at the heart of the compromise between the necessity of compacting DNA in the cell nucleus and the required accessibility to regulatory proteins. The recent availability of genome-wide experimental maps of nucleosome positions for many different organisms and cell types has provided an unprecedented opportunity to elucidate to what extent the DNA sequence conditions the primary structure of chromatin and in turn participates in the chromatin-mediated regulation of nuclear functions, such as gene expression and DNA replication. In this study, we use in vivo and in vitro genome-wide nucleosome occupancy data together with the set of nucleosome-free regions (NFRs) predicted by a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix, to investigate the role of intrinsic nucleosome occupancy in the regulation of the replication spatio-temporal programme in human. We focus our analysis on the so-called replication U/N-domains that were shown to cover about half of the human genome in the germline (skew-N domains) as well as in embryonic stem cells, somatic and HeLa cells (mean replication timing U-domains). The 'master' origins of replication (MaOris) that border these megabase-sized U/N-domains were found to be specified by a few hundred kb wide regions that are hyper-sensitive to DNase I cleavage, hypomethylated, and enriched in epigenetic marks involved in transcription regulation, the hallmarks of localized open chromatin structures. Here we show that replication U/N-domain borders that are conserved in all considered cell lines have an environment highly enriched in nucleosome-excluding-energy barriers, suggesting that these ubiquitous MaOris have been selected during evolution. In contrast, MaOris that are cell-type-specific are mainly regulated epigenetically and are no longer favoured by a local abundance of intrinsic NFRs encoded in the DNA sequence. At the smaller few hundred bp scale of gene promoters, CpG-rich promoters of housekeeping genes found nearby ubiquitous MaOris as well as CpG-poor promoters of tissue-specific genes found nearby cell-type-specific MaOris, both correspond to in vivo NFRs that are not coded as nucleosome-excluding-energy barriers. Whereas the former promoters are likely to correspond to high occupancy transcription factor binding regions, the latter are an illustration that gene regulation in human is typically cell-type-specific.
Collapse
Affiliation(s)
- Guénola Drillon
- Université de Lyon, F-69000 Lyon, France. Laboratoire de Physique, CNRS UMR 5672, École Normale Supérieure de Lyon, F-69007 Lyon, France
| | | | | | | |
Collapse
|
89
|
Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency. PLoS Comput Biol 2015; 11:e1003969. [PMID: 25658386 PMCID: PMC4319821 DOI: 10.1371/journal.pcbi.1003969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 10/06/2014] [Indexed: 11/29/2022] Open
Abstract
Epigenetic regulation of the replication program during mammalian cell differentiation remains poorly understood. We performed an integrative analysis of eleven genome-wide epigenetic profiles at 100 kb resolution of Mean Replication Timing (MRT) data in six human cell lines. Compared to the organization in four chromatin states shared by the five somatic cell lines, embryonic stem cell (ESC) line H1 displays (i) a gene-poor but highly dynamic chromatin state (EC4) associated to histone variant H2AZ rather than a HP1-associated heterochromatin state (C4) and (ii) a mid-S accessible chromatin state with bivalent gene marks instead of a polycomb-repressed heterochromatin state. Plastic MRT regions (≲ 20% of the genome) are predominantly localized at the borders of U-shaped timing domains. Whereas somatic-specific U-domain borders are gene-dense GC-rich regions, 31.6% of H1-specific U-domain borders are early EC4 regions enriched in pluripotency transcription factors NANOG and OCT4 despite being GC poor and gene deserts. Silencing of these ESC-specific “master” replication initiation zones during differentiation corresponds to a loss of H2AZ and an enrichment in H3K9me3 mark characteristic of late replicating C4 heterochromatin. These results shed a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and lineage commitment. During development, embryonic stem cell (ESC) enter a program of cell differentiation eventually leading to all the necessary differentiated cell types. Understanding the mechanisms responsible for the underlying modifications of the gene expression program is of fundamental importance, as it will likely have strong impact on the development of regenerative medicine. We show that besides some epigenetic regulation, ubiquitous master replication origins at replication timing U-domain borders shared by 6 human cell types are transcriptionally active open chromatin regions specified by a local enrichment in nucleosome free regions encoded in the DNA sequence suggesting that they have been selected during evolution. In contrast, ESC specific master replication origins bear a unique epigenetic signature (enrichment in CTCF, H2AZ, NANOG, OCT4, …) likely contributing to maintain ESC chromatin in a highly dynamic and accessible state that is refractory to polycomb and HP1 heterochromatin spreading. These ESC specific master origins thus appear as key genomic regions where epigenetic control of chromatin organization is at play to maintain pluripotency of stem cell lineages and to guide lineage commitment to somatic cell types.
Collapse
|
90
|
Hyrien O. Peaks cloaked in the mist: the landscape of mammalian replication origins. J Cell Biol 2015; 208:147-60. [PMID: 25601401 PMCID: PMC4298691 DOI: 10.1083/jcb.201407004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/16/2014] [Indexed: 12/23/2022] Open
Abstract
Replication of mammalian genomes starts at sites termed replication origins, which historically have been difficult to locate as a result of large genome sizes, limited power of genetic identification schemes, and rareness and fragility of initiation intermediates. However, origins are now mapped by the thousands using microarrays and sequencing techniques. Independent studies show modest concordance, suggesting that mammalian origins can form at any DNA sequence but are suppressed by read-through transcription or that they can overlap the 5' end or even the entire gene. These results require a critical reevaluation of whether origins form at specific DNA elements and/or epigenetic signals or require no such determinants.
Collapse
Affiliation(s)
- Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique UMR8197 and Institut National de la Santé et de la Recherche Médicale U1024, 75005 Paris, France
| |
Collapse
|
91
|
Korthauer KD, Kendziorski C. MADGiC: a model-based approach for identifying driver genes in cancer. ACTA ACUST UNITED AC 2015; 31:1526-35. [PMID: 25573922 PMCID: PMC4426832 DOI: 10.1093/bioinformatics/btu858] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/23/2014] [Indexed: 12/14/2022]
Abstract
Motivation: Identifying and prioritizing somatic mutations is an important and challenging area of cancer research that can provide new insights into gene function as well as new targets for drug development. Most methods for prioritizing mutations rely primarily on frequency-based criteria, where a gene is identified as having a driver mutation if it is altered in significantly more samples than expected according to a background model. Although useful, frequency-based methods are limited in that all mutations are treated equally. It is well known, however, that some mutations have no functional consequence, while others may have a major deleterious impact. The spatial pattern of mutations within a gene provides further insight into their functional consequence. Properly accounting for these factors improves both the power and accuracy of inference. Also important is an accurate background model. Results: Here, we develop a Model-based Approach for identifying Driver Genes in Cancer (termed MADGiC) that incorporates both frequency and functional impact criteria and accommodates a number of factors to improve the background model. Simulation studies demonstrate advantages of the approach, including a substantial increase in power over competing methods. Further advantages are illustrated in an analysis of ovarian and lung cancer data from The Cancer Genome Atlas (TCGA) project. Availability and implementation: R code to implement this method is available at http://www.biostat.wisc.edu/ kendzior/MADGiC/. Contact: kendzior@biostat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Keegan D Korthauer
- Department of Statistics and Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison WI 53706, USA
| | - Christina Kendziorski
- Department of Statistics and Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison WI 53706, USA
| |
Collapse
|
92
|
Chen J, Sun M, Shen B. Deciphering oncogenic drivers: from single genes to integrated pathways. Brief Bioinform 2014; 16:413-28. [PMID: 25378434 DOI: 10.1093/bib/bbu039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
Technological advances in next-generation sequencing have uncovered a wide spectrum of aberrations in cancer genomes. The extreme diversity in cancer mutations necessitates computational approaches to differentiate between the 'drivers' with vital function in cancer progression and those nonfunctional 'passengers'. Although individual driver mutations are routinely identified, mutational profiles of different tumors are highly heterogeneous. There is growing consensus that pathways rather than single genes are the primary target of mutations. Here we review extant bioinformatics approaches to identifying oncogenic drivers at different mutational levels, highlighting the strategies for discovering driver pathways and networks from cancer mutation data. These approaches will help reduce the mutation complexity, thus providing a simplified picture of cancer.
Collapse
|
93
|
Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet 2014; 46:1160-5. [PMID: 25261935 PMCID: PMC4217527 DOI: 10.1038/ng.3101] [Citation(s) in RCA: 373] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/03/2014] [Indexed: 01/05/2023]
Abstract
Cancer primarily develops due to somatic alterations in the genome. Advances in sequencing have enabled large-scale sequencing studies across many tumor types, emphasizing discovery of alterations in protein-coding genes. However, the protein-coding exome comprises less than 2% of the human genome. Here, we analyze complete genome sequences of 863 human tumors from The Cancer Genome Atlas and other sources to systematically identify non-coding regions that are recurrently mutated in cancer. We utilize novel frequency and sequence-based approaches to comprehensively scan the genome for non-coding mutations with potential regulatory impact. We identified recurrent mutations in regulatory elements upstream of PLEKHS1, WDR74, and SDHD, as well as previously identified mutations in the TERT promoter. SDHD promoter mutations are frequent in melanoma and associated with reduced gene expression and poor patient prognosis. The non-protein-coding cancer genome remains widely unexplored and our findings represent a step towards targeting the entire genome for clinical purposes.
Collapse
|
94
|
Fraser HB. Cell-cycle regulated transcription associates with DNA replication timing in yeast and human. Genome Biol 2014; 14:R111. [PMID: 24098959 PMCID: PMC3983658 DOI: 10.1186/gb-2013-14-10-r111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/20/2013] [Indexed: 11/25/2022] Open
Abstract
Background Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to replicate in early S-phase in all plant and animal species studied to date, but this relationship is thought to be absent from both budding yeast and fission yeast. No association between cell-cycle regulated transcription and replication timing has been reported for any species. Results Here I show that in budding yeast, fission yeast, and human, the genes most highly transcribed during S-phase replicate early, whereas those repressed in S-phase replicate late. Transcription during other cell-cycle phases shows either the opposite correlation with replication timing, or no relation. The relationship is strongest near late-firing origins of replication, which is not consistent with a previously proposed model—that replication timing may affect transcription—and instead suggests a potential mechanism involving the recruitment of limiting replication initiation factors during S-phase. Conclusions These results suggest that S-phase transcription may be an important determinant of DNA replication timing across eukaryotes, which may explain the well-established association between transcription and replication timing.
Collapse
|
95
|
Zaghloul L, Drillon G, Boulos RE, Argoul F, Thermes C, Arneodo A, Audit B. Large replication skew domains delimit GC-poor gene deserts in human. Comput Biol Chem 2014; 53 Pt A:153-65. [PMID: 25224847 DOI: 10.1016/j.compbiolchem.2014.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 01/25/2023]
Abstract
Besides their large-scale organization in isochores, mammalian genomes display megabase-sized regions, spanning both genes and intergenes, where the strand nucleotide composition asymmetry decreases linearly, possibly due to replication activity. These so-called skew-N domains cover about a third of the human genome and are bordered by two skew upward jumps that were hypothesized to compose a subset of "master" replication origins active in the germline. Skew-N domains were shown to exhibit a particular gene organization. Genes with CpG-rich promoters likely expressed in the germline are over represented near the master replication origins, with large genes being co-oriented with replication fork progression, which suggests some coordination of replication and transcription. In this study, we describe another skew structure that covers ∼13% of the human genome and that is bordered by putative master replication origins similar to the ones flanking skew-N domains. These skew-split-N domains have a shape reminiscent of a N, but split in half, leaving in the center a region of null skew whose length increases with domain size. These central regions (median size ∼860 kb) have a homogeneous composition, i.e. both a null and constant skew and a constant and low GC content. They correspond to heterochromatin gene deserts found in low-GC isochores with an average gene density of 0.81 promoters/Mb as compared to 7.73 promoters/Mb genome wide. The analysis of epigenetic marks and replication timing data confirms that, in these late replicating heterochomatic regions, the initiation of replication is likely to be random. This contrasts with the transcriptionally active euchromatin state found around the bordering well positioned master replication origins. Altogether skew-N domains and skew-split-N domains cover about 50% of the human genome.
Collapse
Affiliation(s)
- Lamia Zaghloul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Guénola Drillon
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Rasha E Boulos
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Françoise Argoul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Claude Thermes
- Centre de Génétique Moléculaire, CNRS UPR 3404, Gif-sur-Yvette, France
| | - Alain Arneodo
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Benjamin Audit
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.
| |
Collapse
|
96
|
Zhao H, Thienpont B, Yesilyurt BT, Moisse M, Reumers J, Coenegrachts L, Sagaert X, Schrauwen S, Smeets D, Matthijs G, Aerts S, Cools J, Metcalf A, Spurdle A, Amant F, Lambrechts D. Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks. eLife 2014; 3:e02725. [PMID: 25085081 PMCID: PMC4141275 DOI: 10.7554/elife.02725] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA replication errors that persist as mismatch mutations make up the molecular fingerprint of mismatch repair (MMR)-deficient tumors and convey them with resistance to standard therapy. Using whole-genome and whole-exome sequencing, we here confirm an MMR-deficient mutation signature that is distinct from other tumor genomes, but surprisingly similar to germ-line DNA, indicating that a substantial fraction of human genetic variation arises through mutations escaping MMR. Moreover, we identify a large set of recurrent indels that may serve to detect microsatellite instability (MSI). Indeed, using endometrial tumors with immunohistochemically proven MMR deficiency, we optimize a novel marker set capable of detecting MSI and show it to have greater specificity and selectivity than standard MSI tests. Additionally, we show that recurrent indels are enriched for the ‘DNA double-strand break repair by homologous recombination’ pathway. Consequently, DSB repair is reduced in MMR-deficient tumors, triggering a dose-dependent sensitivity of MMR-deficient tumor cultures to DSB inducers. DOI:http://dx.doi.org/10.7554/eLife.02725.001 Before a cell divides, it must first copy all of its genetic material. Any mistakes that are made during this process are called mutations. Mutations can give rise to new traits but are mostly harmful to the cells, or cause cancer; therefore, cells have evolved tools that can efficiently spot these mistakes and repair them. One of the main tools is called mismatch repair (MMR). Defects in the cell's mismatch repair tools can wreak havoc as this allows many mutations to accumulate. Zhao et al. looked at the genomes of tumors where mismatch repair was not working properly to see what makes these ‘MMR-deficient tumors’ different from other tumors. This revealed that MMR-deficient tumors have similar patterns of mutations to those seen in egg and sperm cells. This was unexpected and suggests that mutations that are not corrected by mismatch repair are an important source of the genetic differences found between different humans, and between humans and their ancestors. Identifying cancerous tumors that are MMR-deficient is vital, as these tumors tend not to respond to commonly used cancer treatments. However, current clinical methods to identify MMR-deficient tumors often fail or produce results that are difficult to interpret. MMR-deficient tumors commonly contain mutations called indels, where short fragments of DNA are inserted or deleted into longer DNA sequences. Zhao et al. have found 59 indels that can be used to detect MMR-deficient tumors, where each indel had been identified in several tumors taken from different tissues. This new approach allowed MMR-deficiency to be identified in several types of tumor, including colon and ovarian cancers, with greater sensitivity and accuracy than the existing methods. Zhao et al. also found that the indels in MMR-deficient tumors reduce the ability of the tumors to repair a type of DNA damage called double-strand breaks. In these, both strands of DNA that make up the double helix are broken and the DNA chain is severed. As this kind of damage is very harmful to a cell, making more double-strand breaks could therefore form part of a more effective treatment against MMR-deficient tumors; further research is needed to investigate this possibility. DOI:http://dx.doi.org/10.7554/eLife.02725.002
Collapse
Affiliation(s)
- Hui Zhao
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Betül Tuba Yesilyurt
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Matthieu Moisse
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Joke Reumers
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lieve Coenegrachts
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Xavier Sagaert
- Division of Pathology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Stefanie Schrauwen
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Dominiek Smeets
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Matthijs
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Alex Metcalf
- Division of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Amanda Spurdle
- Division of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | | | - Frederic Amant
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Diether Lambrechts
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| |
Collapse
|
97
|
Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res 2014; 24:1053-63. [PMID: 24823667 PMCID: PMC4079962 DOI: 10.1101/gr.163659.113] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 04/03/2014] [Indexed: 01/27/2023]
Abstract
Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied TranspoSeq, a computational framework that identifies retrotransposon insertions from sequencing data, to whole genomes from 200 tumor/normal pairs across 11 tumor types as part of The Cancer Genome Atlas (TCGA) Pan-Cancer Project. In addition to novel germline polymorphisms, we find 810 somatic retrotransposon insertions primarily in lung squamous, head and neck, colorectal, and endometrial carcinomas. Many somatic retrotransposon insertions occur in known cancer genes. We find that high somatic retrotransposition rates in tumors are associated with high rates of genomic rearrangement and somatic mutation. Finally, we developed TranspoSeq-Exome to interrogate an additional 767 tumor samples with hybrid-capture exome data and discovered 35 novel somatic retrotransposon insertions into exonic regions, including an insertion into an exon of the PTEN tumor suppressor gene. The results of this large-scale, comprehensive analysis of retrotransposon movement across tumor types suggest that somatic retrotransposon insertions may represent an important class of structural variation in cancer.
Collapse
Affiliation(s)
- Elena Helman
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | | | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | - Carrie Sougnez
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Matthew Meyerson
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
- Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
98
|
The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells. PLoS Genet 2014; 10:e1004282. [PMID: 24785686 PMCID: PMC4006723 DOI: 10.1371/journal.pgen.1004282] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 02/18/2014] [Indexed: 11/19/2022] Open
Abstract
The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins. The molecular mechanisms coordinating the activation of about predicted origins remain poorly understood, partly due to the intrinsic rarity of replication bubbles, making it difficult to purify short nascent strands (SNS). The precise identification of origins based on the high-throughput sequencing of SNS constitutes a new methodological challenge. We propose a new statistical method with a controlled resolution, adapted to the detection of replication origins from SNS data. We detected an average of 80,000 replication origins in different cell lines. To evaluate the consistency between different protocols, we compared SNS detections with bubble trapping detections. This comparison demonstrated a good agreement between genome-wide methods, with 65% of SNS-detected origins validated by bubble trapping, and 44% of bubble trapping origins validated by SNS origins, when compared at the same resolution. We investigated the interplay between the spatial and the temporal programs of replication at fine scales. We show that most of the origins detected in regions replicated in early S phase are shared by all the cell lines investigated whereas cell-type-specific origins tend to be replicated in late S phase. We shed a new light on the key role of CpG islands, by showing that 80% of the origins associated with CGIs are constitutive. Our results further show that at least 76% of CGIs are origins of replication. The analysis of associations with chromatin marks at different timing of cell division revealed new potential epigenetic regulators driving the spatiotemporal activity of replication origins. We highlight the potential role of H4K20me1 and H3K27me3, the coupling of which is correlated with increased efficiency of replication origins, clearly identifying those marks as potential key regulators of replication origins. Replication is the mechanism by which genomes are duplicated into two exact copies. Genomic stability is under the control of a spatiotemporal program that orchestrates both the positioning and the timing of firing of about 50,000 replication starting points, also called replication origins. Replication bubbles found at origins have been very difficult to map due to their short lifespan. Moreover, with the flood of data characterizing new sequencing technologies, the precise statistical analysis of replication data has become an additional challenge. We propose a new method to map replication origins on the human genome, and we assess the reliability of our finding using experimental validation and comparison with origins maps obtained by bubble trapping. This fine mapping then allowed us to identify potential regulators of the replication dynamics. Our study highlights the key role of CpG Islands and identifies new potential epigenetic regulators (methylation of lysine 4 on histone H4, and tri-methylation of lysine 27 on histone H3) whose coupling is correlated with an increase in the efficiency of replication origins, suggesting those marks as potential key regulators of replication. Overall, our study defines new potentially important pathways that might regulate the sequential firing of origins during genome duplication.
Collapse
|
99
|
Assié G, Letouzé E, Fassnacht M, Jouinot A, Luscap W, Barreau O, Omeiri H, Rodriguez S, Perlemoine K, René-Corail F, Elarouci N, Sbiera S, Kroiss M, Allolio B, Waldmann J, Quinkler M, Mannelli M, Mantero F, Papathomas T, De Krijger R, Tabarin A, Kerlan V, Baudin E, Tissier F, Dousset B, Groussin L, Amar L, Clauser E, Bertagna X, Ragazzon B, Beuschlein F, Libé R, de Reyniès A, Bertherat J. Integrated genomic characterization of adrenocortical carcinoma. Nat Genet 2014; 46:607-12. [PMID: 24747642 DOI: 10.1038/ng.2953] [Citation(s) in RCA: 465] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/17/2014] [Indexed: 12/15/2022]
Abstract
Adrenocortical carcinomas (ACCs) are aggressive cancers originating in the cortex of the adrenal gland. Despite overall poor prognosis, ACC outcome is heterogeneous. We performed exome sequencing and SNP array analysis of 45 ACCs and identified recurrent alterations in known driver genes (CTNNB1, TP53, CDKN2A, RB1 and MEN1) and in genes not previously reported in ACC (ZNRF3, DAXX, TERT and MED12), which we validated in an independent cohort of 77 ACCs. ZNRF3, encoding a cell surface E3 ubiquitin ligase, was the most frequently altered gene (21%) and is a potential new tumor suppressor gene related to the β-catenin pathway. Our integrated genomic analyses further identified two distinct molecular subgroups with opposite outcome. The C1A group of ACCs with poor outcome displayed numerous mutations and DNA methylation alterations, whereas the C1B group of ACCs with good prognosis displayed specific deregulation of two microRNA clusters. Thus, aggressive and indolent ACCs correspond to two distinct molecular entities driven by different oncogenic alterations.
Collapse
Affiliation(s)
- Guillaume Assié
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Center for Rare Adrenal Diseases, Department of Endocrinology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France. [5]
| | - Eric Letouzé
- 1] Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France. [2]
| | - Martin Fassnacht
- 1] Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, University of Munich, Munich, Germany. [2] Endocrine and Diabetes Unit, Department of Internal Medicine I, University Hospital of Würzburg, Würzburg, Germany. [3] Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Anne Jouinot
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Windy Luscap
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Olivia Barreau
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Center for Rare Adrenal Diseases, Department of Endocrinology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Hanin Omeiri
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Stéphanie Rodriguez
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Karine Perlemoine
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Fernande René-Corail
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Silviu Sbiera
- 1] Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, University of Munich, Munich, Germany. [2] Endocrine and Diabetes Unit, Department of Internal Medicine I, University Hospital of Würzburg, Würzburg, Germany
| | - Matthias Kroiss
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Bruno Allolio
- Endocrine and Diabetes Unit, Department of Internal Medicine I, University Hospital of Würzburg, Würzburg, Germany
| | - Jens Waldmann
- Visceral, Thoracic and Vascular Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Marcus Quinkler
- Department of Clinical Endocrinology, Charité Campus Mitte, Charité University Medicine, Berlin, Germany
| | - Massimo Mannelli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Franco Mantero
- Endocrinology Unit, Department of Medicine, University of Padova, Padova, Italy
| | - Thomas Papathomas
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ronald De Krijger
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Antoine Tabarin
- 1] Department of Endocrinology, Diabetes and Metabolic Diseases, University Hospital of Bordeaux, Bordeaux, France. [2] Rare Adrenal Cancer Network COMETE, Paris, France
| | - Véronique Kerlan
- 1] Rare Adrenal Cancer Network COMETE, Paris, France. [2] Department of Endocrinology, Diabetes and Metabolic Diseases, University Hospital of Brest, Brest, France
| | - Eric Baudin
- 1] Rare Adrenal Cancer Network COMETE, Paris, France. [2] Department of Nuclear Medicine and Endocrine Oncology, Institut Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Frédérique Tissier
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Department of Pathology, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpétrière, Pierre et Marie Curie Université, Paris, France
| | - Bertrand Dousset
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Center for Rare Adrenal Diseases, Department of Endocrinology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France. [5] Department of Digestive and Endocrine Surgery, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Lionel Groussin
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Center for Rare Adrenal Diseases, Department of Endocrinology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Laurence Amar
- Hypertension Unit, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Eric Clauser
- Oncogenetic Laboratory, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Xavier Bertagna
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Center for Rare Adrenal Diseases, Department of Endocrinology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France. [5] Rare Adrenal Cancer Network COMETE, Paris, France
| | - Bruno Ragazzon
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, University of Munich, Munich, Germany
| | - Rossella Libé
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Center for Rare Adrenal Diseases, Department of Endocrinology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France. [5] Rare Adrenal Cancer Network COMETE, Paris, France
| | - Aurélien de Reyniès
- 1] Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France. [2]
| | - Jérôme Bertherat
- 1] INSERM U1016, Institut Cochin, Paris, France. [2] CNRS UMR 8104, Paris, France. [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France. [4] Center for Rare Adrenal Diseases, Department of Endocrinology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France. [5] Rare Adrenal Cancer Network COMETE, Paris, France. [6]
| |
Collapse
|
100
|
Sima J, Gilbert DM. Complex correlations: replication timing and mutational landscapes during cancer and genome evolution. Curr Opin Genet Dev 2014; 25:93-100. [PMID: 24598232 DOI: 10.1016/j.gde.2013.11.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/29/2013] [Indexed: 12/23/2022]
Abstract
A recent flurry of reports correlates replication timing (RT) with mutation rates during both evolution and cancer. Specifically, point mutations and copy number losses correlate with late replication, while copy number gains and other rearrangements correlate with early replication. In some cases, plausible mechanisms have been proposed. Point mutation rates may reflect temporal variation in repair mechanisms. Transcription-induced double-strand breaks are expected to occur in transcriptionally active early replicating chromatin. Fusion partners are generally in close proximity, and chromatin in close proximity replicates at similar times. However, temporal enrichment of copy number gains and losses remains an enigma. Moreover, many conclusions are compromised by a lack of matched RT and sequence datasets, the filtering out of developmental variation in RT, and the use of somatic cell lines to make inferences about germline evolution.
Collapse
Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
| |
Collapse
|