ArticleNucleic acids research2012
3D chromatin conformation correlates with replication timing and is conserved in resting cells.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 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
53 citing papers in PubMed, 95 citations in OpenAlex.
- The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.Nucleic acids research · 2026Article
- DNA methylation and lncRNA control asynchronous DNA replication at specific imprinted gene domains.Nature communications · 2026Article
- From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture.BMC bioinformatics · 2026Article
- Control of epithelial homeostasis by apical polarity: it takes a network.Biochemical Society transactions · 2025Article
- RIF1 controls replication timing in early mouse embryos independently of lamina-associated nuclear organization.Developmental cell · 2025Article
- Replication program of a single-chromosome budding yeast strain.Nucleic acids research · 2025Article
- From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture.bioRxiv : the preprint server for biology · 2025Article
- KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition.Cell reports · 2025Article
- R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania.Nature communications · 2025Article
- Sex-specific DNA-replication in the early mammalian embryo.Nature communications · 2024Article
- Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters.Nature communications · 2024Article
- MLL3/MLL4 enzymatic activity shapes DNA replication timing.bioRxiv : the preprint server for biology · 2023Article
- Locus architecture and RAG scanning determine antibody diversity.Trends in immunology · 2023Review
- Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
- The role of chromatin loop extrusion in antibody diversification.Nature reviews. Immunology · 2022Review
- Breaking the paradigm: early insights from mammalian DNA breakomes.The FEBS journal · 2022Review
- HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries.Nucleic acids research · 2022Article
- Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction.Nature communications · 2021Article
- Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing.International journal of molecular sciences · 2021Article
- Cohesin depleted cells rebuild functional nuclear compartments after endomitosis.Nature communications · 2020Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although chromatin folding is known to be of functional importance to control the gene expression program, less is known regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined with high-throughput sequencing, we identified megabase-sized self-interacting domains in the nucleus of a human lymphoblastoid cell line, as well as in cycling and resting peripheral blood mononuclear cells (PBMC). Strikingly, the boundaries of those domains coincide with early-initiation zones in every cell types. Preferential interactions have been observed between the consecutive early-initiation zones, but also between those separated by several tens of megabases. Thus, the 3D conformation of chromatin is strongly correlated with the replication timing along the whole chromosome. We furthermore provide direct clues that, in addition to the timing value per se, the shape of the timing profile at a given locus defines its set of genomic contacts. As this timing-related scheme of chromatin organization exists in lymphoblastoid cells, resting and cycling PBMC, this indicates that it is maintained several weeks or months after the previous S-phase. Lastly, our work highlights that the major chromatin changes accompanying PBMC entry into cell cycle occur while keeping largely unchanged the long-range chromatin contacts.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.