ArticleCell reports2023
Regulatory architecture of housekeeping genes is driven by promoter assemblies.
Article in Cell reports, 2023. 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
36 citing papers in PubMed, 47 citations in OpenAlex.
- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Current Challenges of Transcription Compartmentalization Research.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Active RNA synthesis patterns nuclear condensates.Cell systems · 2026Article
- A control theoretical approach to gene regulation reveals quantitative constraints for dynamic homeostasis in stochastic gene expression.Biochimica et biophysica acta. Molecular basis of disease · 2026Article
- Transcription condensates are promoter hubs that enhance transcriptional bursts.bioRxiv : the preprint server for 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
- CpG island density predicts CBP/p300 dependency across 3D chromatin clusters.bioRxiv : the preprint server for biology · 2026Article
- 3D-super-enhancers are condensate-associated cis-regulatory communities.Nucleic acids research · 2026Article
- Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.Nature structural & molecular biology · 2026Article
- Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes.The EMBO journal · 2026Article
- Article
- Comprehensive Mapping of Functional Enhancers in Chinese Hamster Ovary Cells.Biotechnology and bioengineering · 2026Article
- Roles of transposable elements and DNA methylation in the formation of CpG islands and CpG-depleted regulatory elements.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The exit from naive pluripotency: a platform for the study of enhancer mechanistics.Biochemical Society transactions · 2025Review
- Article
- TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.Genome biology · 2025Article
- Transcription regulation by biomolecular condensates.Nature reviews. Molecular cell biology · 2025Review
- Liquid condensates: a new barrier to loop extrusion?Cellular and molecular life sciences : CMLS · 2025Review
- Pioneer factor GATA6 promotes colorectal cancer through 3D genome regulation.Science advances · 2025Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 1 country.
Funding
Abstract
Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.
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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.