Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells

Abstract

Genomic mapping of DNA replication origins (ORIs) in mammals provides a powerful means for understanding the regulatory complexity of our genome. Here we combine a genome-wide approach to identify preferential sites of DNA replication initiation at 0.4% of the mouse genome with detailed molecular analysis at distinct classes of ORIs according to their location relative to the genes. Our study reveals that 85% of the replication initiation sites in mouse embryonic stem (ES) cells are associated with transcriptional units. Nearly half of the identified ORIs map at promoter regions and, interestingly, ORI density strongly correlates with promoter density, reflecting the coordinated organisation of replication and transcription in the mouse genome. Detailed analysis of ORI activity showed that CpG island promoter-ORIs are the most efficient ORIs in ES cells and both ORI specification and firing efficiency are maintained across cell types. Remarkably, the distribution of replication initiation sites at promoter-ORIs exactly parallels that of transcription start sites (TSS), suggesting a co-evolution of the regulatory regions driving replication and transcription. Moreover, we found that promoter-ORIs are significantly enriched in CAGE tags derived from early embryos relative to all promoters. This association implies that transcription initiation early in development sets the probability of ORI activation, unveiling a new hallmark in ORI efficiency regulation in mammalian cells.

Epigenetic regulation of the human genome: coherence between promoter activity and large-scale chromatin environment

“…In contrast, progress in elucidating the chromatin-mediated control of replication origin usage and efficiency as well as of the maintenance of the spatio-temporal replication program in higher eukaryotes has been rather slow (Berezney et al 2000;Bogan et al 2000;Gilbert 2001Gilbert , 2010Méchali 2001Méchali , 2010Bell & Dutta 2002;McNairn & Gilbert 2003;Aladjem 2007;Courbet et al 2008;Hamlin et al 2008). Only very recently nascent DNA strands synthesized at origins were purified by various methods to map replication origins genome-wide in mouse (Sequeira-Mendes et al 2009;Cayrou et al 2011) and human (Lucas et al 2007;Cadoret et al 2008;Karnani et al 2010;Martin et al 2011;Mesner et al 2011;Valenzuela et al 2011). The set of replication origins identified so far are strongly associated with annotated promoters and seem to be enriched in transcription factor binding sites (Cadoret et al 2008;Karnani et al 2010;Besnard et al 2012) and in CpG islands (Cadoret et al 2008;Sequeira-Mendes et al 2009;Cayrou et al 2011).…”

“…Only very recently nascent DNA strands synthesized at origins were purified by various methods to map replication origins genome-wide in mouse (Sequeira-Mendes et al 2009;Cayrou et al 2011) and human (Lucas et al 2007;Cadoret et al 2008;Karnani et al 2010;Martin et al 2011;Mesner et al 2011;Valenzuela et al 2011). The set of replication origins identified so far are strongly associated with annotated promoters and seem to be enriched in transcription factor binding sites (Cadoret et al 2008;Karnani et al 2010;Besnard et al 2012) and in CpG islands (Cadoret et al 2008;Sequeira-Mendes et al 2009;Cayrou et al 2011). But the correlation to transcription is not that obvious since a significant proportion of origins are found in regions void of DNase-I-hypersensitive sites (DHSs) and of histone marks found at active promoters (Cadoret et al 2008;Maric & Prioleau 2010).…”

Analysis of a Drosophila amplicon in follicle cells highlights the diversity of metazoan replication origins

“…Despite their diverse approaches, recent origin mapping studies have all found that replication origins and ORC binding sites closely correspond to gene regions, specifically the transcription start sites of actively transcribed genes (8,10,11). The relationship between active transcription and DNA replication initiation remains unclear, however.…”

“…However, there has been a tremendous increase in the number of metazoan origins identified recently, due to the application of methods to select origincentered DNA and detection by microarray and high-throughput sequencing technologies (6)(7)(8)(9)(10)(11)(12). These origin datasets have enabled correlative analyses to genome-wide features such as transcription, epigenetic modifications, and replication timing.…”

Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 – 15, 2016 - Strasbourg, France

“…33 Comparison of ORI location with the chromatin landscape revealed a negative correlation between ORIs and DNA methylation and a positive one between ORIs and canonical marks of active chromatin, as observed in mammalian cells. 34,35 Interestingly, while most ORIs preferentially colocalize with genes, around 10% of them are present in heterochromatin and associate with particular classes of TE in both non-pericentromeric and pericentromeric regions. A major challenge ahead will be to identify ORIs in the whole plant, a project that is being pursued using Short Nascent Strands (SNS)-seq purified from seedlings.…”