ArticleProceedings of the National Academy of Sciences of the United States of America2012
Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- APC loss promotes endometrial cancer progression by upregulating FGF12 expression: An integrated multi-omics analysis.Chinese medical journal · 2026Article
- Master transcription-factor binding sites constitute the core of early replication control elements.The EMBO journal · 2025Article
- Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.Cell · 2022Article
- Mapping the evolving landscape of super-enhancers during cell differentiation.Genome biology · 2021Article
- Mammalian DNA Replication Timing.Cold Spring Harbor perspectives in biology · 2021Review
- Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency.Stem cell reports · 2020Review
- Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots.PLoS genetics · 2020Article
- Transcription factors: building hubs in the 3D space.Cell cycle (Georgetown, Tex.) · 2020Review
- Control of DNA replication timing in the 3D genome.Nature reviews. Molecular cell biology · 2019Review
- Replication timing alterations in leukemia affect clinically relevant chromosome domains.Blood advances · 2019Article
- Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.Stem cell reports · 2019Article
- Review
- Article
- Multi-scale structural community organisation of the human genome.BMC bioinformatics · 2017Article
- Anatomy of Mammalian Replication Domains.Genes · 2017Review
- Dynamics of plant DNA replication based on PCNA visualization.Scientific reports · 2016Article
- Replicating Large Genomes: Divide and Conquer.Molecular cell · 2016Review
- Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation.Scientific reports · 2016Article
- Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.Molecular cell · 2016Article
- Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells.Genome research · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Several 400- to 800-kb murine chromosome domains switch from early to late replication during loss of pluripotency, accompanied by a stable form of gene silencing that is resistant to reprogramming. We found that, whereas enhanced nuclease accessibility correlated with early replication genome-wide, domains that switch replication timing during differentiation were exceptionally inaccessible even when early-replicating. Nonetheless, two domains studied in detail exhibited substantial changes in transcriptional activity and higher-order chromatin unfolding confined to the region of replication timing change. Chromosome conformation capture (4C) data revealed that in the unfolded state in embryonic stem cells, these domains interacted preferentially with the early-replicating chromatin compartment, rarely interacting even with flanking late-replicating domains, whereas after differentiation, these same domains preferentially associated with late-replicating chromatin, including flanking domains. In both configurations they retained local boundaries of self-interaction, supporting the replication domain model of replication-timing regulation. Our results reveal a principle of developmentally regulated, large-scale chromosome folding involving a subnuclear compartment switch of inaccessible chromatin. This unusual level of regulation may underlie resistance to reprogramming in replication-timing switch regions.
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