ArticlePLoS biology2010
Poised transcription factories prime silent uPA gene prior to activation.
Article in PLoS biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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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.
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Who cites it
48 citing papers in PubMed, 85 citations in OpenAlex.
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- Epigenetic regulatory layers in the 3D nucleus.Molecular cell · 2024Review
- Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture.Cold Spring Harbor perspectives in biology · 2022Review
- RNA polymerase II clusters form in line with surface condensation on regulatory chromatin.Molecular systems biology · 2021Article
- Understanding 3D genome organization by multidisciplinary methods.Nature reviews. Molecular cell biology · 2021Review
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- Methods for mapping 3D chromosome architecture.Nature reviews. Genetics · 2020Review
- "Looping In" Mechanics: Mechanobiologic Regulation of the Nucleus and the Epigenome.Advanced healthcare materials · 2020Review
- RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.Molecular systems biology · 2017Article
- Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.Nature communications · 2017Article
- Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.Nature structural & molecular biology · 2017Article
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- Chromatin organization in pluripotent cells: emerging approaches to study and disrupt function.Briefings in functional genomics · 2016Review
- Morphology of nuclear transcription.Histochemistry and cell biology · 2016Review
- Analysis of a transgenic Oct4 enhancer reveals high fidelity long-range chromosomal interactions.Scientific reports · 2015Article
- Three-dimensional genome architecture: players and mechanisms.Nature reviews. Molecular cell biology · 2015Review
- Myosin VI regulates gene pairing and transcriptional pause release in T cells.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei.Journal of experimental botany · 2015Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
The position of genes in the interphase nucleus and their association with functional landmarks correlate with active and/or silent states of expression. Gene activation can induce chromatin looping from chromosome territories (CTs) and is thought to require de novo association with transcription factories. We identify two types of factory: "poised transcription factories," containing RNA polymerase II phosphorylated on Ser5, but not Ser2, residues, which differ from "active factories" associated with phosphorylation on both residues. Using the urokinase-type plasminogen activator (uPA) gene as a model system, we find that this inducible gene is predominantly associated with poised (S5p(+)S2p(-)) factories prior to activation and localized at the CT interior. Shortly after induction, the uPA locus is found associated with active (S5p(+)S2p(+)) factories and loops out from its CT. However, the levels of gene association with poised or active transcription factories, before and after activation, are independent of locus positioning relative to its CT. RNA-FISH analyses show that, after activation, the uPA gene is transcribed with the same frequency at each CT position. Unexpectedly, prior to activation, the uPA loci internal to the CT are seldom transcriptionally active, while the smaller number of uPA loci found outside their CT are transcribed as frequently as after induction. The association of inducible genes with poised transcription factories prior to activation is likely to contribute to the rapid and robust induction of gene expression in response to external stimuli, whereas gene positioning at the CT interior may be important to reinforce silencing mechanisms prior to induction.
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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.