ArticleGenes & development2011
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.
Article in Genes & development, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 209 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.
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Who cites it
209 citing papers in PubMed, 308 citations in OpenAlex.
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- SEC Mediates mAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- From chromatin dynamics to brain disease: Polycomb-Trithorax mechanisms in neurodevelopment.Trends in neurosciences · 2026Review
- SP1 antagonizes H3K27me3 to shape chromatin landscapes for RNA polymerase II recruitment during gastrulation.Nucleic acids research · 2026Article
- Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo.Developmental cell · 2026Article
- MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution.Genome medicine · 2025Article
- Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling.The EMBO journal · 2024Article
- Epigenetic control and manipulation of neuronal maturation timing.Current opinion in genetics & development · 2024Review
- Transcriptional elongation control in developmental gene expression, aging, and disease.Molecular cell · 2023Review
- DOT1L is a barrier to histone acetylation during reprogramming to pluripotency.Science advances · 2023Article
- RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation.Developmental cell · 2023Article
- RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation.medRxiv : the preprint server for health sciences · 2023Article
- Article
- The regulation of transcription elongation in embryonic stem cells.Frontiers in cell and developmental biology · 2023Review
- KAS-Analyzer: a novel computational framework for exploring KAS-seq data.Bioinformatics advances · 2023Article
- Integrative analysis reveals histone demethylase LSD1 promotes RNA polymerase II pausing.iScience · 2022Article
- Long-distance association of topological boundaries through nuclear condensates.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Relationships between genome-wide R-loop distribution and classes of recurrent DNA breaks in neural stem/progenitor cells.Scientific reports · 2022Article
- DDB1 prepares brown adipocytes for cold-induced thermogenesis.Life metabolism · 2022Article
- CDK9 activity switch associated with AFF1 and HEXIM1 controls differentiation initiation from epidermal progenitors.Nature communications · 2022Article
149 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
6 authors at 1 institution in 1 country.
Funding
Abstract
Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genome's primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally engaged RNA polymerases in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ∼40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol II's entry into elongation. Furthermore, "bivalent" ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb group complexes PRC1 (Polycomb-repressive complex 1) and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5' proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation.
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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.