Programa dinâmico predizível do tempo da replicação do DNA em células humanas

quarta-feira, novembro 18, 2009

Predictable dynamic program of timing of DNA replication in human cells

Romain Desprat1, Danielle Thierry-Mieg2, Nathalie Lailler1, Julien Lajugie1, Carl Schildkraut3,4, Jean Thierry-Mieg2 and Eric E. Bouhassira1,2,3,4

+ Author Affiliations

1Department of Medicine and Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA;

2NCBI, National Institutes of Health, Bethesda, Maryland 20894, USA;

3Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA

Abstract

The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replication forks progress unidirectionally from origins that can be hundreds of kilobases away. Absence of initiation in one transition region is shown at the molecular level by single molecule analysis of replicated DNA (SMARD). Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarters of S phase. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue-specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid-firing origins are located near moderately expressed genes, and that late-firing origins are located far from genes.

Footnotes

↵4 Corresponding authors.

E-mail eric.bouhassira@einstein.yu.edu; fax (718) 430-8855.

E-mail carl.schildkraut@einstein.yu.edu; fax (718) 430-8574.

[Supplemental material is available online at http://www.genome.org. The sequence data and the microarray data from this study have been submitted to NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession no. GSE18679.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.094060.109.

Received March 21, 2009.

Accepted September 8, 2009.

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