ReviewNucleic acids research2018
Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations.
Review in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed, 125 citations in OpenAlex.
- The molecular basis of transcription initiation by RNA polymerase II.Nature reviews. Molecular cell biology · 2026Review
- Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- A machine learning framework predicts oncogenic driver mutations from SNP profiles in lung adenocarcinoma.Discover oncology · 2026Article
- Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes.The EMBO journal · 2026Article
- Cell-cycle-related transcriptional factor DLX4: a novel prognostic biomarker and potential therapeutic target in colorectal cancer.Cancer cell international · 2025Article
- Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription.Physical review letters · 2025Article
- Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity.Nature communications · 2025Article
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Article
- Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structure.Cell genomics · 2024Article
- Diverse epistatic effects in barley-powdery mildew interactions localize to host chromosome hotspots.iScience · 2024Article
- Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.Nature communications · 2024Article
- Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies.Current opinion in genetics & development · 2023Review
- Review
- Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion.Nature genetics · 2023Article
- Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis.Journal of animal science and biotechnology · 2023Article
- MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network.Cell reports methods · 2023Article
- The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation.Developmental cell · 2023Article
- Surfactancy in a tadpole model of proteins.Journal of the Royal Society, Interface · 2022Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and topologically-associating domains (TADs), to contact domains stabilized by cohesin and CTCF. However, molecular mechanisms underlying this folding, and the way folding affects transcriptional activity, remain obscure. Here we review physical principles driving proteins bound to long polymers into clusters surrounded by loops, and present a parsimonious yet comprehensive model for the way the organization determines function. We argue that clusters of active RNA polymerases and their transcription factors are major architectural features; then, contact domains, TADs and compartments just reflect one or more loops and clusters. We suggest tethering a gene close to a cluster containing appropriate factors-a transcription factory-increases the firing frequency, and offer solutions to many current puzzles concerning the actions of enhancers, super-enhancers, boundaries and eQTLs (expression quantitative trait loci). As a result, the activity of any gene is directly influenced by the activity of other transcription units around it in 3D space, and this is supported by Brownian-dynamics simulations of transcription factors binding to cognate sites on long polymers.
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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.