Over half of the human genome is comprised of repetitive DNA organized as gene-poor, late replicating, transcriptionally silent heterochromatin. Recent studies suggest that there is a widespread opening of chromatin at repeated regions during carcinogenesis and aging. Given the total amount of repetitive DNA and the tendency of sequences in open chromatin to more readily serve as replication origins, these chromatin changes could significantly perturb global genome replication by outcompeting other regions of the genome for limiting replication factors. Indeed, our data from budding yeast suggest that increasing the efficiency of origin firing at repetitive sequences impairs DNA replication across the genome. In this proposal we use Saccharomyces cerevisiae to test our model that nucleosome re-positioning promotes the recruitment of initiation factors to replication origins in repetitive sequences and furthermore, that activation of origins in these repetitive sequences compromises the replication and stability of unique portions of the genome. S. cerevisiae is an excellent system in which to perform these tests: the major repetitive sequence, the ribosomal DNA (rDNA) is composed of homogenous tandem repeats (150 copies), each containing a potential origin of replication whose function is sensitive to chromatin context. Moreover, the sequence specificity of yeast origins creates uniform and predictable positioning of replication initiation factors and nucleosomes in their vicinity, greatly facilitating application and interpretation of a deep sequencing method for epigenomic profiling that we have developed. Our results will provide insights into the mechanisms by which chromatin and nucleosome positioning modulate replication origins at repetitive sequences and will shed light on the largely unexplored phenomenon of intra-genomic competition for replication resources as a mechanism that shapes global replication.

Public Health Relevance

Over half of the human genome is composed of repeated gene-free sequences. We have evidence from yeast demonstrating that particular genetic and environmental changes allow repeated sequences to compete with the rest of the genome for limiting replication resources, to the detriment of genome replication. In this proposal, we will test a model for how changes in chromosome structure affect this competition, why this competition is detrimental to genome replication, and how this competition may underlie important biological phenomena like cellular aging.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics B Study Section (MGB)
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Reddy, Michael K
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Fred Hutchinson Cancer Research Center
United States
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Foss, Eric J; Lao, Uyen; Bedalov, Antonio (2018) G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome. J Vis Exp :
Foss, Eric J; Lao, Uyen; Dalrymple, Emily et al. (2017) SIR2 suppresses replication gaps and genome instability by balancing replication between repetitive and unique sequences. Proc Natl Acad Sci U S A 114:552-557