ArticleNucleic acids research2018
The RNA exosome contributes to gene expression regulation during stem cell differentiation.
Article 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 36 papers.
What it found
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Who cites it
36 citing papers in PubMed, 58 citations in OpenAlex.
- Mapping and quantifying nascent transcript start sites using TT-TSS-seq.Genome research · 2026Article
- Synergy between regulatory elements can render cohesin dispensable for distal enhancer function.Science (New York, N.Y.) · 2026Article
- EXOSC3 knockdown induces G1/S phase arrest to suppress hepatocellular carcinoma cell proliferation.Scientific reports · 2025Article
- Ontogenetic stage and type of donor cells shape extracellular vesicles' therapeutic potential for osteoarthritis.Stem cell research & therapy · 2025Article
- RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation.BMC biology · 2025Article
- Enhancing cardiac regeneration: direct reprogramming of fibroblasts into myocardial-like cells using extracellular vesicles secreted by cardiomyocytes.Molecular and cellular biochemistry · 2025Article
- The alcohol exposome.Alcohol (Fayetteville, N.Y.) · 2025Review
- Exosomal Epigenetics.EMBnet.journal · 2024Article
- Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation.Molecular cell · 2023Article
- Exosomes induce neurogenesis of pluripotent P19 cells.Stem cell reviews and reports · 2023Article
- Downregulation of a tumor suppressor gene LKB1 in lung transplantation as a biomarker for chronic murine lung allograft rejection.Cellular immunology · 2023Article
- PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave.The Plant cell · 2022Article
- Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells.Nucleic acids research · 2022Article
- Ultraefficient extracellular vesicle-guided direct reprogramming of fibroblasts into functional cardiomyocytes.Science advances · 2022Article
- RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response.Life science alliance · 2022Article
- Exosomes in pathogenesis, diagnosis, and treatment of pulmonary fibrosis.Frontiers in pharmacology · 2022Review
- Distinct transcription kinetics of pluripotent cell states.Molecular systems biology · 2022Article
- Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function.International journal of molecular sciences · 2021Review
- Aberrant expression of MYD88 via RNA-controlling CNOT4 and EXOSC3 in colonic mucosa impacts generation of colonic cancer.Cancer science · 2021Article
- Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness.Nature genetics · 2021Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription versus RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. Depletion of the nuclear exosome cofactor RBM7 leads to similar effects. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.
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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.