Journal
CELL
Volume 159, Issue 5, Pages 1015-1026Publisher
CELL PRESS
DOI: 10.1016/j.cell.2014.10.025
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Funding
- National Human Genome Research Institute [R01 HG 006855]
- Integra-Life Seventh Framework Programme [315997]
- Stanley Center for Psychiatric Research
- Howard Hughes Medical Institute
- Harvard Stem Cell Institute
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Genomic DNA replicates in a choreographed temporal order that impacts the distribution of mutations along the genome. We show here that DNA replication timing is shaped by genetic polymorphisms that act in cis upon megabase-scale DNA segments. In genome sequences from proliferating cells, read depth along chromosomes reflected DNA replication activity in those cells. We used this relationship to analyze variation in replication timing among 161 individuals sequenced by the 1000 Genomes Project. Genome-wide association of replication timing with genetic variation identified 16 loci at which inherited alleles associate with replication timing. We call these replication timing quantitative trait loci (rtQTLs). rtQTLs involved the differential use of replication origins, exhibited allele-specific effects on replication timing, and associated with gene expression variation at megabase scales. Our results show replication timing to be shaped by genetic polymorphism and identify a means by which inherited polymorphism regulates the mutability of nearby sequences.
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