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.
Lamia Zaghloul 1, 2; Antoine Baker 1, 2; Benjamin Audit 1, 2; Alain Arneodo 1, 2
@article{CRMECA_2012__340_11-12_745_0,
author = {Lamia Zaghloul and Antoine Baker and Benjamin Audit and Alain Arneodo},
title = {Gene organization inside replication domains in mammalian genomes},
journal = {Comptes Rendus. M\'ecanique},
pages = {745--757},
publisher = {Elsevier},
volume = {340},
number = {11-12},
year = {2012},
doi = {10.1016/j.crme.2012.10.023},
language = {en},
}
TY - JOUR AU - Lamia Zaghloul AU - Antoine Baker AU - Benjamin Audit AU - Alain Arneodo TI - Gene organization inside replication domains in mammalian genomes JO - Comptes Rendus. Mécanique PY - 2012 SP - 745 EP - 757 VL - 340 IS - 11-12 PB - Elsevier DO - 10.1016/j.crme.2012.10.023 LA - en ID - CRMECA_2012__340_11-12_745_0 ER -
%0 Journal Article %A Lamia Zaghloul %A Antoine Baker %A Benjamin Audit %A Alain Arneodo %T Gene organization inside replication domains in mammalian genomes %J Comptes Rendus. Mécanique %D 2012 %P 745-757 %V 340 %N 11-12 %I Elsevier %R 10.1016/j.crme.2012.10.023 %G en %F CRMECA_2012__340_11-12_745_0
Lamia Zaghloul; Antoine Baker; Benjamin Audit; Alain Arneodo. Gene organization inside replication domains in mammalian genomes. Comptes Rendus. Mécanique, Out of Equilibrium Dynamics, 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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