ArticleiScience2021
Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin.
Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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Who cites it
6 citing papers in PubMed, 10 citations in OpenAlex.
- Organ-Specific and Conserved Regulatory Logic Orchestrates Gene Expression in the Embryonic Mesothelium.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genetic Regulation of Alternative Polyadenylation Provides Novel Insights into Molecular Mechanisms Underlying Non-small Cell Lung Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic acids research · 2024Article
- Inferring CTCF-binding patterns and anchored loops across human tissues and cell types.Patterns (New York, N.Y.) · 2023Article
- The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data.Bioinformatics (Oxford, England) · 2023Article
- 3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin.STAR protocols · 2022Article
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Context-specific activities of transcription regulators (TRs) in the nucleus modulate spatiotemporal gene expression precisely. Using the largest ChIP-seq data and chromatin loops in the human K562 cell line, we initially interrogated TR cooperation in 3D chromatin via a graphical model and revealed many known and novel TRs manipulating context-specific pathways. To explore TR cooperation across broad tissue/cell types, we systematically leveraged large-scale open chromatin profiles, computational footprinting, and high-resolution chromatin interactions to investigate tissue/cell type-specific TR cooperation. We first delineated a landscape of TR cooperation across 40 human tissue/cell types. Network modularity analyses uncovered the commonality and specificity of TR cooperation in different conditions. We also demonstrated that TR cooperation information can better interpret the disease-causal variants identified by genome-wide association studies and recapitulate cell states during neural development. Our study characterizes shared and unique patterns of TR cooperation associated with the cell type specificity of gene regulation in 3D chromatin.
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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 OpenQuestion graph.