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Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):E4810-9. doi: 10.1073/pnas.1609060113. Epub 2016 Jul 19.

Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers.

Author information

1
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; INSERM, U1016, Institut Cochin, 75014 Paris, France; CNRS, UMR8104, 75014 Paris, France; Universite Paris Descartes, Sorbonne Paris Cite, 75006 Paris, France;
2
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
3
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; kevin@hms.harvard.edu.

Abstract

The origin recognition complex (ORC) binds sites from which DNA replication is initiated. We address ORC binding selectivity in vivo by mapping ∼52,000 ORC2 binding sites throughout the human genome. The ORC binding profile is broader than those of sequence-specific transcription factors, suggesting that ORC is not bound or recruited to specific DNA sequences. Instead, ORC binds nonspecifically to open (DNase I-hypersensitive) regions containing active chromatin marks such as H3 acetylation and H3K4 methylation. ORC sites in early and late replicating regions have similar properties, but there are far more ORC sites in early replicating regions. This suggests that replication timing is due primarily to ORC density and stochastic firing of origins. Computational simulation of stochastic firing from identified ORC sites is in accord with replication timing data. Large genomic regions with a paucity of ORC sites are strongly associated with common fragile sites and recurrent deletions in cancers. We suggest that replication origins, replication timing, and replication-dependent chromosome breaks are determined primarily by the genomic distribution of activator proteins at enhancers and promoters. These activators recruit nucleosome-modifying complexes to create the appropriate chromatin structure that allows ORC binding and subsequent origin firing.

KEYWORDS:

DNA replication; ORC; chromatin; replication origins; replication timing

PMID:
27436900
PMCID:
PMC4995967
DOI:
10.1073/pnas.1609060113
[Indexed for MEDLINE]
Free PMC Article

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