ArticleNature communications2023
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers.
What it found
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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
120 citing papers in PubMed.
- Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase.eLife · 2026Article
- Single-molecule chromatin tracing reveals a diversity of megabase heterochromatin domains.Nature structural & molecular biology · 2026Article
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Characterization of Protein Co-Localization and Histone Modifications at Enhancers Anchored in Chromatin Loops.Biology · 2026Article
- High-resolution chromatin mapping reveals that CTCF anchors meiotic loops to the chromosome axis.Nature communications · 2026Article
- Human body single-cell atlas of three-dimensional genome organization and DNA methylation.Science (New York, N.Y.) · 2026Article
- Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).Nature protocols · 2026Review
- Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026Article
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation.bioRxiv : the preprint server for biology · 2026Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin.bioRxiv : the preprint server for biology · 2026Article
- Power-law penalties correct distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions.NAR genomics and bioinformatics · 2026Article
- Metadomain and metaloop genome interactions in mammalian T cells.Cell reports · 2026Article
- Resolving Sub-Nuclear Architecture from Compartments to Functional Domains.International journal of molecular sciences · 2026Review
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies.Cell genomics · 2026Article
- Condensin IDC has a functional ATPase that is required for X-Chromosome dosage compensation in C. elegans.Genetics · 2026Article
60 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors.
Funding
Abstract
Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.
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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.