ArticleGenes & development2014
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation.
Article in Genes & development, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers, 1 of them a synthesis that pooled it.
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Who cites it
165 citing papers in PubMed, 1 synthesis or guideline pooled it, 332 citations in OpenAlex.
- Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions.Epigenetics & chromatin · 2018Pooled it
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- Unexpected nuclear hormone receptor and chromatin dynamics regulate estrous cycle dependent gene expression.Nucleic acids research · 2024Article
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- Identifying topologically associating domains using differential kernels.PLoS computational biology · 2024Article
- LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells.The EMBO journal · 2024Article
- Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.Bioinformatics (Oxford, England) · 2024Article
- Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries.Nucleic acids research · 2024Article
- A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families.BMC biology · 2024Article
- Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.Life science alliance · 2024Article
- Long-range gene regulation in hormone-dependent cancer.Nature reviews. Cancer · 2023Review
- SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease.Nature communications · 2023Article
105 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human genome is segmented into topologically associating domains (TADs), but the role of this conserved organization during transient changes in gene expression is not known. Here we describe the distribution of progestin-induced chromatin modifications and changes in transcriptional activity over TADs in T47D breast cancer cells. Using ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing), Hi-C (chromosome capture followed by high-throughput sequencing), and three-dimensional (3D) modeling techniques, we found that the borders of the ∼ 2000 TADs in these cells are largely maintained after hormone treatment and that up to 20% of the TADs could be considered as discrete regulatory units where the majority of the genes are either transcriptionally activated or repressed in a coordinated fashion. The epigenetic signatures of the TADs are homogeneously modified by hormones in correlation with the transcriptional changes. Hormone-induced changes in gene activity and chromatin remodeling are accompanied by differential structural changes for activated and repressed TADs, as reflected by specific and opposite changes in the strength of intra-TAD interactions within responsive TADs. Indeed, 3D modeling of the Hi-C data suggested that the structure of TADs was modified upon treatment. The differential responses of TADs to progestins and estrogens suggest that TADs could function as "regulons" to enable spatially proximal genes to be coordinately transcribed in response to hormones.
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