ArticleNature communications2016
Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 40 citations in OpenAlex.
- The Role of Transient Crosslinks in the Chromatin Search Response to DNA Damage.International journal of molecular sciences · 2025Article
- Centromeres are stress-induced fragile sites.Current biology : CB · 2025Article
- The power of weak, transient interactions across biology: A paradigm of emergent behavior.Physica D. Nonlinear phenomena · 2023Article
- Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Molecular cell · 2023Review
- Centromeres: From chromosome biology to biotechnology applications and synthetic genomes in plants.Plant biotechnology journal · 2022Review
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO.Nature communications · 2022Article
- Review
- Integrative approaches in genome structure analysis.Structure (London, England : 1993) · 2022Review
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture.Frontiers in genetics · 2021Article
- Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development.Frontiers in immunology · 2021Review
- Lamina-associated domains: peripheral matters and internal affairs.Genome biology · 2020Review
- Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions.Nature communications · 2019Article
- Druggable Transcriptional Networks in the Human Neurogenic Epigenome.Pharmacological reviews · 2019Review
- Predicting three-dimensional genome organization with chromatin states.PLoS computational biology · 2019Article
- Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes.Nature communications · 2019Article
- Finding Friends in the Crowd: Three-Dimensional Cliques of Topological Genomic Domains.Frontiers in genetics · 2019Review
- Producing genome structure populations with the dynamic and automated PGS software.Nature protocols · 2018Article
- Computational 3D genome modeling using Chrom3D.Nature protocols · 2018Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as 'Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures.
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Registered trials
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.