ArticleNucleic acids research2020
The RNA exosome shapes the expression of key protein-coding genes.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 16 citations in OpenAlex.
- Review
- Mechanisms of transcription termination across the coding and noncoding loci of the genome.Nature reviews. Molecular cell biology · 2026Review
- Article
- True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end status.Nucleic acids research · 2025Article
- Nuclear mRNA decay: regulatory networks that control gene expression.Nature reviews. Genetics · 2024Review
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- RNA-regulatory exosome complex suppresses an apoptotic program to confer erythroid progenitor cell survival in vivo.Blood advances · 2023Article
- Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting.NAR genomics and bioinformatics · 2022Article
- Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics.Nature reviews. Molecular cell biology · 2022Review
- Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression.Molecular cell · 2022Article
- Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3' end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.
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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.