ArticleNature communications2023
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors.
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 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- Chiron3D: an interpretable deep learning framework for understanding the DNA code of chromatin looping.Bioinformatics (Oxford, England) · 2026Article
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- The ChIP-FRiP pipeline quantifies co-binding and reveals how antibody background contributes to cohesin ChIP-seq patterns.bioRxiv : the preprint server for biology · 2026Article
- Dissecting the contribution of transposable elements to interphase chromosome structure.Genome biology · 2026Article
- The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE.Nature communications · 2025Article
- Liquid condensates: a new barrier to loop extrusion?Cellular and molecular life sciences : CMLS · 2025Review
- 4D Genome Analysis Using PHi-C2.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPy.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Exploring Contact Distance Distributions with Google Colaboratory.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Extracting Chromosome Structural Information as One-Dimensional Metrics and Integrating Them with Epigenomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1.EMBO reports · 2024Article
- An extrinsic motor directs chromatin loop formation by cohesin.The EMBO journal · 2024Article
- The Wild West of spike-in normalization.Nature biotechnology · 2024Article
- Nitrogen K-edge X-ray adsorption near-edge structure spectroscopy of chemically adsorbed ammonia gas on clay minerals and theAnalytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2024Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.
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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.