ArticlePLoS computational biology2012
Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 75 citations in OpenAlex.
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- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.Nature protocols · 2023Review
- Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation.Nucleic acids research · 2022Article
- Genome-wide mapping of individual replication fork velocities using nanopore sequencing.Nature communications · 2022Article
- Organization of DNA Replication Origin Firing inGenes · 2021Article
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- Genome duplication ineLife · 2020Article
- Bayesian inference of origin firing time distributions, origin interference and licencing probabilities from Next Generation Sequencing data.Nucleic acids research · 2019Article
- Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations.Nature genetics · 2019Article
- Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions.Nucleic acids research · 2018Article
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- Epigenetic Transitions and Knotted Solitons in Stretched Chromatin.Scientific reports · 2017Article
- Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand.Genome research · 2017Article
- Multi-scale structural community organisation of the human genome.BMC bioinformatics · 2017Article
- APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context.Genome research · 2017Article
- Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq).Nucleic acids research · 2016Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- The mutation spectrum in genomic late replication domains shapes mammalian GC content.Nucleic acids research · 2016Article
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14 authors at 7 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In higher eukaryotes, replication program specification in different cell types remains to be fully understood. We show for seven human cell lines that about half of the genome is divided in domains that display a characteristic U-shaped replication timing profile with early initiation zones at borders and late replication at centers. Significant overlap is observed between U-domains of different cell lines and also with germline replication domains exhibiting a N-shaped nucleotide compositional skew. From the demonstration that the average fork polarity is directly reflected by both the compositional skew and the derivative of the replication timing profile, we argue that the fact that this derivative displays a N-shape in U-domains sustains the existence of large-scale gradients of replication fork polarity in somatic and germline cells. Analysis of chromatin interaction (Hi-C) and chromatin marker data reveals that U-domains correspond to high-order chromatin structural units. We discuss possible models for replication origin activation within U/N-domains. The compartmentalization of the genome into replication U/N-domains provides new insights on the organization of the replication program in the human genome.
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