ArticlePLoS computational biology2015
Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 24 citations in OpenAlex.
- Nuclear-localized, iron-bound superoxide dismutase-2 antagonizes epithelial lineage programs to promote stemness of breast cancer cells via a histone demethylase activity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Role of the Histone Variant H2A.Z in Metazoan Development.Journal of developmental biology · 2022Review
- Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing.International journal of molecular sciences · 2021Article
- Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints.Nucleic acids research · 2019Article
- Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions.Nucleic acids research · 2018Article
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Multi-scale structural community organisation of the human genome.BMC bioinformatics · 2017Article
- Crosstalk between pluripotency factors and higher-order chromatin organization.Nucleus (Austin, Tex.) · 2016Review
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations.Scientific reports · 2016Article
- Metaboloepigenetic Regulation of Pluripotent Stem Cells.Stem cells international · 2016Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenetic regulation of the replication program during mammalian cell differentiation remains poorly understood. We performed an integrative analysis of eleven genome-wide epigenetic profiles at 100 kb resolution of Mean Replication Timing (MRT) data in six human cell lines. Compared to the organization in four chromatin states shared by the five somatic cell lines, embryonic stem cell (ESC) line H1 displays (i) a gene-poor but highly dynamic chromatin state (EC4) associated to histone variant H2AZ rather than a HP1-associated heterochromatin state (C4) and (ii) a mid-S accessible chromatin state with bivalent gene marks instead of a polycomb-repressed heterochromatin state. Plastic MRT regions (≲ 20% of the genome) are predominantly localized at the borders of U-shaped timing domains. Whereas somatic-specific U-domain borders are gene-dense GC-rich regions, 31.6% of H1-specific U-domain borders are early EC4 regions enriched in pluripotency transcription factors NANOG and OCT4 despite being GC poor and gene deserts. Silencing of these ESC-specific "master" replication initiation zones during differentiation corresponds to a loss of H2AZ and an enrichment in H3K9me3 mark characteristic of late replicating C4 heterochromatin. These results shed a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and lineage commitment.
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