CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis.
Copy number variation (CNV) in the human genome is of vital importance to human health and evolution of our species. However, much of the molecular basis of CNV mutagenesis remains to be elucidated. Considering the DNA replication model of 'fork stalling and template switching' for CNV formation, we hypothesized that replication fork progression could be important for CNV mutagenesis. However, molecular assays of replication fork progression at the genome level are technically challenging. Instead, we conducted an estimation of DNA replication dynamics, as the statistic R, using the readily available data of replication timing. Small R-values can reflect 'slowed' replication, which could result from less fork initiation, reduced fork speed or fork barriers. We generated genome-wide profiles of R in the genomes of human, mouse and Drosophila. Intriguingly, the CNV breakpoints in all three genomes showed significantly biased distributions toward the genomic regions with small R-values, suggesting potential replication stress-induced CNV instability. Notably, among the human CNVs with distinct breakpoint junction characteristics, the homology-mediated and VNTR-mediated CNVs contribute the most to the correlation between CNV instability and the statistic R, consistent with the recent findings in the C. elegans and yeast genomes of repeat-induced DNA replication error and consequent CNV formation. The statistic R may reflect both replication stress and the effect of local genome architecture on fork progression. Our concordant observations suggest an important role for DNA replicative mechanisms in CNV mutagenesis and genome instability.
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and.
Lu
L
Chen
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and.
Weichen
W
Zhou
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and.
Cheng
C
Zhang
Department of Molecular and Human Genetics and Department of Pediatrics, Baylor College of Medicine, Houston TX 77030, USA Texas Children's Hospital, Houston, TX 77030, USA.
James R
JR
Lupski
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.
Li
L
Jin
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China, zhangfeng@fudan.edu.cn.
Feng
F
Zhang
D000818:Animals; D056915:DNA Copy Number Variations; D004261:DNA Replication; D004330:Drosophila / Q000235:genetics; D016678:Genome; D042822:Genomic Instability; D006801:Humans; D051379:Mice