Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

Gaetano Ivan Dellino; Davide Cittaro; Rossana Piccioni; Lucilla Luzi; Stefania Banfi; Simona Segalla; Matteo Cesaroni; Ramiro Mendoza-Maldonado; Mauro Giacca; Pier Giuseppe Pelicci

doi:10.1101/gr.142331.112

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

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

↵Present addresses: ⁶Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, 20132 Milan, Italy;
↵7 Humanitas Clinical and Research Center, 20089 Rozzano (MI), Italy;
↵8 Department of Oncology, San Raffaele Scientific Institute, 20132 Milan, Italy;
↵9 The Wistar Institute, Philadelphia, PA 19104, USA;
↵10 National Laboratory CIB, Area Science Park, 34149 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

↵11 Corresponding authors

E-mail gaetano.dellino{at}ieo.eu

E-mail piergiuseppe.pelicci{at}ieo.eu
[Supplemental material is available for this article.]
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.

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