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Series GSE119488 Query DataSets for GSE119488
Status Public on Mar 06, 2019
Title Evolution of Replication Origins in Vertebrate Genomes: Rapid Turnover Despite Selective Constraints [SNS-seq]
Organism Gallus gallus
Experiment type Other
Summary Background: The replication program of vertebrate genomes is driven by the chromosomal distribution and timing of activation of ten of thousands replication origins. Genome-wide studies have shown the frequent association of origins with promoters and CpG islands, and their enrichment in G-quadruplexes sequence motifs (G4). However the genetic determinants driving their activity remain poorly understood. To gain insight on functional constraints operating on replication origins and on their spatial distribution, we conduct 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 a ∼ 40bp region centered on the replication initiation loci. Surprisingly, this depletion in genetic diversity is not linked to the presence of G4 motifs, nor to the association with promoters or CpG islands. In contrast, we also show that origins have experienced a rapid turnover during vertebrates evolution, since pairwise comparisons of origin maps revealed that only 4 to 24% of them are conserved between any two species.
Conclusions: This study unravels the existence of a novel genetic determinant of replication origins, whose precise functional role 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.
 
Overall design Short Nascent Strand sequencing of the DT40 chicken cell line
 
Contributor(s) Massip F, Laurent M, Brossas C, Fernández-Justel JM, Gómez M, Prioleau M, Duret L, Picard F
Citation(s) 30916335
Submission date Sep 05, 2018
Last update date Jun 05, 2019
Contact name Florian Massip
E-mail(s) florian.massip@gmail.com
Organization name Max Delbrueck Center for Molecular Medicin
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platforms (1)
GPL19787 Illumina NextSeq 500 (Gallus gallus)
Samples (1)
GSM3375591 DT40_SNS-seq
Relations
BioProject PRJNA489388
SRA SRP159637

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE119488_RAW.tar 890.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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