Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing
- Gaetano Ivan Dellino1,2,11,
- Davide Cittaro3,6,
- Rossana Piccioni1,
- Lucilla Luzi4,
- Stefania Banfi1,7,
- Simona Segalla1,8,
- Matteo Cesaroni1,9,
- Ramiro Mendoza-Maldonado5,10,
- Mauro Giacca5 and
- Pier Giuseppe Pelicci1,2,11
- 1Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy;
- 2Dipartimento di Scienze della Salute, University of Milano, 20122 Milan, Italy;
- 3IIT@SEMM, IFOM-IEO Campus, 20141 Milan, Italy;
- 4IFOM-FIRC Institute of Molecular Oncology, 20139 Milan, Italy;
- 5ICGEB International Centre for Genetic Engineering and Biotechnology, 34134 Trieste, Italy
Abstract
We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G1 and the probability of firing during S.
Footnotes
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↵11 Corresponding authors
E-mail gaetano.dellino{at}ieo.eu
E-mail piergiuseppe.pelicci{at}ieo.eu
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.142331.112.
- Received April 26, 2012.
- Accepted September 25, 2012.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
