ArticleNucleic acids research2015
Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 37 citations in OpenAlex.
- 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
- On the molecular basis of enduring memory in neurons, and cell fate in fibroblasts.Nucleic acids research · 2026Review
- Two distinct chromatin modules regulate proinflammatory gene expression.Nature cell biology · 2026Article
- RNA polymerase II transcription compartments - from factories to condensates.Nature reviews. Genetics · 2025Review
- Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor.Aging cell · 2024Article
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- circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner.RNA (New York, N.Y.) · 2022Article
- Liquid-Liquid Phase Separation in Chromatin.Cold Spring Harbor perspectives in biology · 2022Review
- RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis.Science advances · 2021Article
- Article
- Higher-Order Chromatin Regulation of Inflammatory Gene Expression.Mediators of inflammation · 2017Review
- Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity.Nucleic acids research · 2016Article
- Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response.Genome research · 2016Article
- Super-resolution measurement of distance between transcription sites using RNA FISH with intronic probes.Methods (San Diego, Calif.) · 2016Article
- Morphology of nuclear transcription.Histochemistry and cell biology · 2016Review
- Enhancers as non-coding RNA transcription units: recent insights and future perspectives.Nature reviews. Genetics · 2016Review
- RNA as a fundamental component of interphase chromosomes: could repeats prove key?Current opinion in genetics & development · 2016Review
- βlinc1 encodes a long noncoding RNA that regulates islet β-cell formation and function.Genes & development · 2016Article
- Isolation of the protein and RNA content of active sites of transcription from mammalian cells.Nature protocols · 2016Article
- Phase Behavior of DNA in the Presence of DNA-Binding Proteins.Biophysical journal · 2016Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
Abstract
While mapping total and poly-adenylated human transcriptomes has now become routine, characterizing nascent transcripts remains challenging, largely because nascent RNAs have such short half-lives. Here, we describe a simple, fast and cost-effective method to isolate RNA associated with transcription factories, the sites responsible for the majority of nuclear transcription. Following stimulation of human endothelial cells with the pro-inflammatory cytokine TNFα, we isolate and analyse the RNA content of factories by sequencing. Comparison with total, poly(A)(+) and chromatin RNA fractions reveals that sequencing of purified factory RNA maps the complete nascent transcriptome; it is rich in intronic unprocessed transcript, as well as long intergenic non-coding (lincRNAs) and enhancer-associated RNAs (eRNAs), micro-RNA precursors and repeat-derived RNAs. Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts.
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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.