Evolution of Replication Origins in Vertebrate Genomes: Rapid Turnover Despite Selective Constraints

Abstract

Background:The replication programme of vertebrate genomes is driven by the chromosomal distribution and timing of activation of tens of thousands of replication origins. Genome-wide studies have shown the frequent association of origins with promoters and CpG islands, and their enrichment in G-quadruplex sequence motifs (G4). However, the genetic determinants driving their activity remain poorly understood. To gain insight on the functional constraints operating on replication origins and their spatial distribution, we conducted the first evolutionary comparison of genome-wide origins maps across vertebrates. Results:We generated a high resolution genome-wide map of chicken replication origins (the first of a bird genome), and performed an extensive comparison with human and mouse maps. The analysis of intra-species polymorphism revealed a strong depletion of genetic diversity on an ∼ 40 bp region centred on the replication initiation loci. Surprisingly, this depletion in genetic diversity was not linked to the presence of G4 motifs, nor to the association with promoters or CpG islands. In contrast, we also showed that origins experienced a rapid turnover during vertebrates evolution, since pairwise comparisons of origin maps revealed that only 4 to 24% of them were conserved between any two species. Conclusions:This study unravels the existence of a novel genetic determinant of replication origins, the precise functional role of which remains to be determined. Despite the importance of replication initiation activity for the fitness of organisms, the distribution of replication origins along vertebrate chromosomes is highly flexible.

A predictable conserved DNA base composition signature defines human core DNA replication origins

“…3h). This is in accordance with the presence of an origin G-rich Repeated Element (OGRE) 2 or tandemly arranged multiple (up to 6-12) G4 structures as well as ultra-short C/G-rich nucleotide motifs found at human, mouse and chicken origins 35 .…”

Clustering of strong replicators associated with active promoters is sufficient to establish an early‐replicating domain

“…RT profiles obtained from S1 to S4 fractions showed that the IZ about 30 kb upstream of the site of insertion (IZ.1) is activated in S3 in WT cells, whereas the IZ located 60 kb downstream (IZ.2) is activated already in S2. IZ.1 and IZ.2 correspond to strong initiation sites detected by the short nascent strand (SNS) assay (Massip et al , 2019). Profiles observed at the same region in a cell line modified on both chromosomes (2 × ( β A ‐globin + β‐actin ) cell line) showed firing of the IZ.1 in S1, whereas the IZ.2 is unchanged compared to the WT cell line.…”

“…NS‐enriched and depleted regions for each fraction are represented in purple and blue, respectively. Single reads form SNS aligned and track of replication origins (Ori peaks) determined in (Massip et al , 2019) are reported in between. The three mid‐late insertion sites 1, 2, and 3 are indicated with red arrows.…”

“…The three sites chosen for insertion are indicated with red arrows and dotted lines (mid‐late, late 1 (A), and late 2 (B) insertion). At the bottom, an enlargement of late insertion sites (chr1: 69,500,000–71,500,000 (A), chr1: 177,000,000–179,000,000 (B); galGal5), displaying genes, mRNAs and ESTs for the chicken and all other species together with track of replication origins determined in (Massip et al , 2019) (Ori peaks) is shown. Tracks of RefSeq genes are represented in blue, tracks of Ensembl genes in red, tracks of AUGUSTUS ab initio gene predictions and TransMap alignements in green and tracks of mRNAs and ESTs in black.…”

The enrichment of breakpoints in late-replicating chromatin provides novel insights into chromoanagenesis mechanisms

“…RefSeq genes coordinates were extracted from the UCSC Genome Browser; pLi scores were extracted from the gnomAD dataset (Lek et al 2016). Annotation was also made across lamina associated domains (LADs) (Guelen et al 2008); topologically associated domains (TADs) (Rao et al 2014); repeated elements (RepeatMasker); chromosomal cytoband and Giemsa staining (Furey and Haussler 2003); chromosomal common fragile sites (Fungtammasan et al 2012); replication origins (Massip et al 2019); A/B compartments (Fortin and Hansen 2015) and replication timing (Dixon et al 2018). For the latter, only constitutive early and late domains were considered.…”