ArticlePLoS genetics2017
Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex.
Article in PLoS genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 54 citations in OpenAlex.
- Review
- Ribosomal RNA synthesis by RNA polymerase I is subject to premature termination of transcription.eLife · 2026Article
- RiboCop surveils pre-rRNA processing by Dicer in cellular quiescence.bioRxiv : the preprint server for biology · 2025Article
- Article
- High resolution landscape of ribosomal RNA processing and surveillance.Nucleic acids research · 2024Article
- The circular logic of mRNA homeostasis.Transcription · 2023Review
- In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2023Article
- Maturation of small nucleolar RNAs: from production to function.RNA biology · 2023Review
- MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus.Nucleic acids research · 2022Article
- Hydrogen-deuterium exchange mass spectrometry of Mtr4 with diverse RNAs reveals substrate-dependent dynamics and interfaces in the arch.Nucleic acids research · 2022Article
- Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis.Genes & development · 2022Article
- Antisense ribosomal siRNAs inhibit RNA polymerase I-directed transcription in C. elegans.Nucleic acids research · 2021Article
- A budding yeast model for human disease mutations in theRNA (New York, N.Y.) · 2021Article
- Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- System-wide analyses of the fission yeast poly(A)Genome research · 2020Article
- Substrate specificity of the TRAMP nuclear surveillance complexes.Nature communications · 2020Article
- Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit.Nucleic acids research · 2020Article
- RNA Exosomes and Their Cofactors.Methods in molecular biology (Clifton, N.J.) · 2020Review
- Global Identification of Human Exosome Substrates Using RNA Interference and RNA Sequencing.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Mapping Exosome-Substrate Interactions In Vivo by UV Cross-Linking.Methods in molecular biology (Clifton, N.J.) · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA. Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but it was unclear how many substrates follow each pathway in vivo. We used CRAC (UV crosslinking and analysis of cDNA) in growing cells to identify transcriptome-wide interactions of RNAs with the major nuclear exosome-cofactor Mtr4 and with individual exosome subunits (Rrp6, Csl4, Rrp41 and Rrp44) along the threaded RNA path. We compared exosome complexes lacking Rrp44 exonuclease activity, carrying a mutation in the Rrp44 S1 RNA-binding domain predicted to disfavor direct access, or with multiple mutations in Rrp41 reported to impede RNA access to the central channel in vitro. Preferential use of channel-threading was seen for mRNAs, 5S rRNA, scR1 (SRP) and aborted tRNAs transcripts. Conversely, pre-tRNAs preferentially accessed Rrp44 directly. Both routes participated in degradation and maturation of RNAPI transcripts, with hand-over during processing. Rrp41 mutations blocked substrate passage through the channel to Rrp44 only for cytoplasmic mRNAs, supporting the predicted widening of the lumen in the Rrp6-associated, nuclear complex. Many exosome substrates exhibited clear preferences for a specific path to Rrp44. Other targets showed redundancy, possibly allowing the efficient handling of highly diverse RNA-protein complexes and RNA structures. Both threading and direct access routes involve the RNA helicase Mtr4. mRNAs that are predominately nuclear or cytoplasmic exosome substrates can be distinguished in vivo.
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Registered trials
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