ArticleGenome research2016
Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 208 papers, 1 of them a synthesis that pooled it.
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Who cites it
208 citing papers in PubMed, 1 synthesis or guideline pooled it, 400 citations in OpenAlex.
- (Re)defining the human chromatome: an integrated meta-analysis of localization, function, abundance, physical properties, and domain composition of chromatin proteins.Nucleic acids research · 2026Pooled it
- Synthetic Regulatory Genomics.Annual review of genomics and human genetics · 2026Review
- Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.Nucleic acids research · 2026Article
- APC loss promotes endometrial cancer progression by upregulating FGF12 expression: An integrated multi-omics analysis.Chinese medical journal · 2026Article
- The Many Faces of SetDB1.Epigenomes · 2026Review
- Novel principles of molecular genetic mapping of the interphase genome of Drosophila melanogaster.G3 (Bethesda, Md.) · 2026Article
- Article
- 3D-super-enhancers are condensate-associated cis-regulatory communities.Nucleic acids research · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- ZAD mediates chromatin binding and insulator activity of Drosophila Pita and can be replaced with the human ZFP276 ZAD-like domain.Epigenetics & chromatin · 2025Article
- Prediction of Enhancer RNAs in Chicken Genome.International journal of molecular sciences · 2025Article
- Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF.Scientific reports · 2025Article
- The length and strength of compartmental interactions are modulated by condensin II activity.PLoS genetics · 2025Article
- A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs.BMC genomics · 2025Article
- Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila.Genome biology · 2025Article
- A Joint Analysis of RNA-DNA and DNA-DNA Interactomes Reveals Their Strong Association.International journal of molecular sciences · 2025Article
- Current progress and future perspective of super-enhancers: a viable and effective bridge between the transcriptional apparatus and disease.Frontiers in genetics · 2025Review
- The Role of Lamins in Genome Organisation: A Modelling Perspective.Sub-cellular biochemistry · 2025Review
148 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)(+) RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.
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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.