ArticleCell2012
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Article in Cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 810 papers.
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Who cites it
810 citing papers in PubMed.
- A cardiac-related, promoter-proximal, regulatory element shapes chromatin and JAG1 transcription.Life science alliance · 2026Article
- 3D chromatin organisation contributes to the regulatory logic in differentiating lymphatic endothelium.EMBO reports · 2026Article
- Article
- cPRC1.2 and CTCF-mediated transition from poised to active chromatin loops at bivalent genes.EMBO reports · 2026Article
- Methylation Mesa define functional regulatory elements for targeted gene activation.Nature communications · 2026Article
- 3D epigenomic landscape of the human retinal pigment epithelium.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer.Genome biology · 2026Article
- EBER-associated promoter contacts mark accessible but transcriptionally constrained RNAPII promoter hubs in EBV-positive B cells.Epigenetics & chromatin · 2026Article
- Epigenetic compartmentalization of mitotic chromosomes by phase-separation-driven repulsion between WDR5 and the chromosomal passenger complex.Nature communications · 2026Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells.Genome biology · 2026Article
- Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes.bioRxiv : the preprint server for biology · 2026Article
- The exonic SNP rs11676272-C risk allele mediates diet-induced obesity and reduces enhancer activation.EMBO reports · 2026Article
- Low birth weight, DNA methylation patterns in cord blood, and inflammation at birth.Translational pediatrics · 2026Article
- MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis.Science advances · 2026Article
- NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells.PLoS genetics · 2026Article
- HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets.bioRxiv : the preprint server for biology · 2026Article
- Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.Nature structural & molecular biology · 2026Article
- Review
750 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
36 authors.
Funding
Abstract
Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.
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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.