Allele-specific analysis of DNA replication origins in mammalian cells

Boris A. Bartholdy, Rituparna Mukhopadhyay, Julien Lajugie, Mirit I. Aladjem, Eric E. Bouhassira

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

The mechanisms that control the location and timing of firing of replication origins are poorly understood. Using a novel functional genomic approach based on the analysis of SNPs and indels in phased human genomes, we observe that replication asynchrony is associated with small cumulative variations in the initiation efficiency of multiple origins between the chromosome homologues, rather than with the activation of dormant origins. Allele-specific measurements demonstrate that the presence of G-quadruplex-forming sequences does not correlate with the efficiency of initiation. Sequence analysis reveals that the origins are highly enriched in sequences with profoundly asymmetric G/C and A/T nucleotide distributions and are almost completely depleted of antiparallel triplex-forming sequences. We therefore propose that although G4-forming sequences are abundant in replication origins, an asymmetry in nucleotide distribution, which increases the propensity of origins to unwind and adopt non-B DNA structure, rather than the ability to form G4, is directly associated with origin activity.

Original languageEnglish (US)
Article number7051
JournalNature Communications
Volume6
DOIs
StatePublished - May 19 2015

Fingerprint

Replication Origin
DNA Replication
Nucleotides
deoxyribonucleic acid
Alleles
Cells
G-Quadruplexes
DNA
Human Genome
Chromosomes
Single Nucleotide Polymorphism
Sequence Analysis
Genes
Chemical activation
nucleotides
genome
chromosomes
time measurement
asymmetry
activation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

Allele-specific analysis of DNA replication origins in mammalian cells. / Bartholdy, Boris A.; Mukhopadhyay, Rituparna; Lajugie, Julien; Aladjem, Mirit I.; Bouhassira, Eric E.

In: Nature Communications, Vol. 6, 7051, 19.05.2015.

Research output: Contribution to journalArticle

Bartholdy, Boris A. ; Mukhopadhyay, Rituparna ; Lajugie, Julien ; Aladjem, Mirit I. ; Bouhassira, Eric E. / Allele-specific analysis of DNA replication origins in mammalian cells. In: Nature Communications. 2015 ; Vol. 6.
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