ArticleCell reports2022
Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription.
Article in Cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease.iScience · 2026Article
- Quantitative Control of Transposable Elements: From Genome Plasticity to Immune Regulatory Circuits.Cell biochemistry and function · 2026Review
- T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset.NAR genomics and bioinformatics · 2026Article
- UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility.Nucleic acids research · 2026Article
- Hierarchical Chromatin Rewiring Orchestrates Early Transcriptional Regulation in Mouse Cerebral Cortex Following Focal Ischemia.bioRxiv : the preprint server for biology · 2026Article
- Identity rather than 3D position informs splicing of rare introns in the human genome.iScience · 2026Article
- Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.Communications biology · 2026Article
- Stress-responsive nucleus accumbens dopamine D2 receptor-expressing neurons modulate cocaine-induced behavioral sensitization.Frontiers in cellular neuroscience · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Interplay Between 3D Chromatin Architecture and Gene Regulation at theInternational journal of molecular sciences · 2025Article
- Differential regulation of mesoscale chromosome conformations in osteoblasts and osteosarcoma.Genome biology · 2025Article
- Aberrant Enhancer Regulation, Phase Separation, and Autoimmune Diseases.Clinical reviews in allergy & immunology · 2025Review
- Context-dependent regulatory variants in Alzheimer's disease.bioRxiv : the preprint server for biology · 2025Article
- HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data.Briefings in bioinformatics · 2025Article
- Genetic coupling of enhancer activity and connectivity in gene expression control.Nature communications · 2025Article
- Gaussian processes for time series with lead-lag effects with applications to biology data.Biometrics · 2025Article
- Regulatory T cell therapies: from patient data to biological insights.Frontiers in immunology · 2025Review
- Non-coding variation in dementias: mechanisms, insights, and challenges.NPJ dementia · 2025Review
- Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease.bioRxiv : the preprint server for biology · 2024Article
- GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly spaced time points of macrophage activation. Enhancers and genes connected by loops exhibit stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. At these looped enhancer-promoter pairs, changes in acetylation at distal enhancers precede changes in gene expression. Changes in gene expression exhibit a directional bias at differential loop anchors; gained loops are associated with increased expression of genes oriented away from the center of the loop, and lost loops are often accompanied by high levels of transcription within the loop boundaries themselves. These results are consistent with a reciprocal relationship where loops can facilitate increased transcription by connecting promoters to distal enhancers, whereas high levels of transcription can impede loop formation.
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