A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation
TLDR
It is proposed that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR) that will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.Abstract:
Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2–5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3′ tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.read more
Citations
More filters
Journal ArticleDOI
The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End-Joining Pathway
TL;DR: Patients lacking normal NHEJ are not only sensitive to ionizing radiation (IR), but also severely immunodeficient in the range of DNA end substrate configurations upon which they can act.
Journal ArticleDOI
Mechanisms of change in gene copy number
TL;DR: Current models of the mechanisms that cause copy number variation focus on perturbation of DNA replication and replication of non-contiguous DNA segments and cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
Journal ArticleDOI
Structural Variation in the Human Genome and its Role in Disease
TL;DR: The discovery of submicroscopic copy-number variations (CNVs) present in the authors' genomes has changed dramatically their perspective on DNA structural variation and disease and it is now thought that CNVs encompass more total nucleotides and arise more frequently than SNPs.
Journal ArticleDOI
Copy number variation in human health, disease, and evolution.
TL;DR: Copy number variation, especially gene duplication and exon shuffling, can be a predominant mechanism driving gene and genome evolution and appear much higher for CNVs than for SNPs.
Journal ArticleDOI
CNVs: harbingers of a rare variant revolution in psychiatric genetics.
Dheeraj Malhotra,Jonathan Sebat +1 more
TL;DR: The genetic bases of neuropsychiatric disorders are beginning to yield to scientific inquiry and genome-wide studies of copy number variation (CNV) have given rise to a new understanding of disease etiology, bringing rare variants to the forefront.
References
More filters
Book
DNA Repair and Mutagenesis
TL;DR: Nucleotide excision repair in mammalian cells: genes and proteins Mismatch repair The SOS response and recombinational repair in prokaryotes Mutagenesis in proKaryote Mutagenisation in eukaryotes Other DNA damage tolerance responses in eUKaryotes.
Journal ArticleDOI
Global variation in copy number in the human genome
Richard Redon,Shumpei Ishikawa,Karen R. Fitch,Lars Feuk,George H. Perry,T. Daniel Andrews,Heike Fiegler,Michael H. Shapero,Andrew R. Carson,Wenwei Chen,Eun Kyung Cho,Stephanie Dallaire,Jennifer L. Freeman,Juan R. González,Mònica Gratacòs,Jing Huang,Dimitrios Kalaitzopoulos,Daisuke Komura,Jeffrey R. MacDonald,Christian R. Marshall,Rui Mei,Lyndal Montgomery,Keunihiro Nishimura,Kohji Okamura,Fan Shen,Martin J. Somerville,Joelle Tchinda,Armand Valsesia,Cara Woodwark,Fengtang Yang,Junjun Zhang,Tatiana Zerjal,Jane Zhang,Lluís Armengol,Donald F. Conrad,Xavier Estivill,Chris Tyler-Smith,Nigel P. Carter,Hiroyuki Aburatani,Charles Lee,Keith W. Jones,Stephen W. Scherer,Matthew E. Hurles +42 more
TL;DR: A first-generation CNV map of the human genome is constructed through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia, underscoring the importance of CNV in genetic diversity and evolution and the utility of this resource for genetic disease studies.
Journal ArticleDOI
Detection of large-scale variation in the human genome.
A. John Iafrate,Lars Feuk,Miguel Rivera,Miguel Rivera,Marc L. Listewnik,Patricia K. Donahoe,Ying Qi,Stephen W. Scherer,Charles Lee,Charles Lee +9 more
TL;DR: This article identified 255 loci across the human genome that contain genomic imbalances among unrelated individuals, and revealed that half of these regions overlap with genes, and many coincide with segmental duplications or gaps in human genome assembly.
Journal ArticleDOI
Large-Scale Copy Number Polymorphism in the Human Genome
Jonathan Sebat,B. Lakshmi,Jennifer Troge,Joan Alexander,Janet M. Young,Pär Lundin,Susanne Månér,Hillary Massa,Megan Walker,Maoyen Chi,Nicholas Navin,Robert Lucito,John Healy,James W. Hicks,Kenny Q. Ye,Andrew Reiner,T. Conrad Gilliam,Barbara J. Trask,Nick Patterson,Anders Zetterberg,Michael Wigler +20 more
TL;DR: It is shown that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans.
Related Papers (5)
A DNA Replication Mechanism for Generating Nonrecurrent Rearrangements Associated with Genomic Disorders
Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development
Philip J. Stephens,Christopher Greenman,Beiyuan Fu,Fengtang Yang,Graham R. Bignell,Laura Mudie,Erin Pleasance,King Wai Lau,David Beare,Lucy Stebbings,Stuart McLaren,Meng-Lay Lin,David J. McBride,Ignacio Varela,Serena Nik-Zainal,Catherine Leroy,Mingming Jia,Andrew Menzies,Adam Butler,Jon W. Teague,Michael A. Quail,John Burton,Harold Swerdlow,Nigel P. Carter,Laura Morsberger,Christine A. Iacobuzio-Donahue,George A. Follows,Anthony R. Green,Adrienne M. Flanagan,Adrienne M. Flanagan,Michael R. Stratton,P. Andrew Futreal,Peter J. Campbell,Peter J. Campbell +33 more