Comptes Rendus
Gene organization inside replication domains in mammalian genomes
Comptes Rendus. Mécanique, Volume 340 (2012) no. 11-12, pp. 745-757.

We investigate the large-scale organization of human genes with respect to “master” replication origins that were previously identified as bordering nucleotide compositional skew domains. We separate genes in two categories depending on their CpG enrichment at the promoter which can be considered as a marker of germline DNA methylation. Using expression data in mouse, we confirm that CpG-rich genes are highly expressed in germline whereas CpG-poor genes are in a silent state. We further show that, whether tissue-specific or broadly expressed (housekeeping genes), the CpG-rich genes are over-represented close to the replication skew domain borders suggesting some coordination of replication and transcription. We also reveal that the transcription of the longest CpG-rich genes is co-oriented with replication fork progression so that the promoter of these transcriptionally active genes be located into the accessible open chromatin environment surrounding the master replication origins that border the replication skew domains. The observation of a similar gene organization in the mouse genome confirms the interplay of replication, transcription and chromatin structure as the cornerstone of mammalian genome architecture.

Published online:
DOI: 10.1016/j.crme.2012.10.023
Keywords: Gene organization, Replication domains, Gene length, Chromatin structure

Lamia Zaghloul 1, 2; Antoine Baker 1, 2; Benjamin Audit 1, 2; Alain Arneodo 1, 2

1 Université de Lyon, 69000 Lyon, France
2 Laboratoire de Physique, ENS de Lyon, CNRS, 46, allée dʼItalie, 69007 Lyon, France
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     title = {Gene organization inside replication domains in mammalian genomes},
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Lamia Zaghloul; Antoine Baker; Benjamin Audit; Alain Arneodo. Gene organization inside replication domains in mammalian genomes. Comptes Rendus. Mécanique, Volume 340 (2012) no. 11-12, pp. 745-757. doi : 10.1016/j.crme.2012.10.023. https://comptes-rendus.academie-sciences.fr/mecanique/articles/10.1016/j.crme.2012.10.023/

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