ArticleNucleic acids research2023
Hi-TrAC detects active sub-TADs and reveals internal organizations of super-enhancers.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 13 citations in OpenAlex.
- Elucidation of chromatin loops among regulatory regions using Hi-TrAC.Frontiers in epigenetics and epigenomics · 2026Article
- Optimal CXCR5 expression during Tfh maturation involves the Bhlhe40-Pou2af1 axis.Cell reports · 2025Article
- Utilizing Omic Data to Understand Integrative Physiology.Physiology (Bethesda, Md.) · 2025Review
- BLIMP1 negatively regulates IL-2 signaling in T cells.Science advances · 2025Article
- Liquid condensates: a new barrier to loop extrusion?Cellular and molecular life sciences : CMLS · 2025Review
- Structural heterogeneity and functional convergence of transposable elements.Frontiers in genetics · 2025Article
- Memory CD4+ T cells sequentially restructure their 3D genome during stepwise activation.Frontiers in cell and developmental biology · 2025Article
- TAD-dependent sub-TAD is required for enhancer-promoter interaction enabling the β-globin transcription.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- Review
- Three-dimensional chromatin reorganization regulates B cell development during ageing.Nature cell biology · 2024Article
- TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene.Nature communications · 2024Article
- Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction.Immunity · 2024Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The spatial folding of eukaryotic genome plays a key role in genome function. We report here that our recently developed method, Hi-TrAC, which specializes in detecting chromatin loops among accessible genomic regions, can detect active sub-TADs with a median size of 100 kb, most of which harbor one or two cell specifically expressed genes and regulatory elements such as super-enhancers organized into nested interaction domains. These active sub-TADs are characterized by highly enriched histone mark H3K4me1 and chromatin-binding proteins, including Cohesin complex. Deletion of selected sub-TAD boundaries have different impacts, such as decreased chromatin interaction and gene expression within the sub-TADs or compromised insulation between the sub-TADs, depending on the specific chromatin environment. We show that knocking down core subunit of the Cohesin complex using shRNAs in human cells or decreasing the H3K4me1 modification by deleting the H3K4 methyltransferase Mll4 gene in mouse Th17 cells disrupted the sub-TADs structure. Our data also suggest that super-enhancers exist as an equilibrium globule structure, while inaccessible chromatin regions exist as a fractal globule structure. In summary, Hi-TrAC serves as a highly sensitive and inexpensive approach to study dynamic changes of active sub-TADs, providing more explicit insights into delicate genome structures and functions.
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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 Socratic graph.