PXD017114

PXD017114 is an original dataset announced via ProteomeXchange.

Title	Substrate Specificity of the TRAMP Nuclear Surveillance Complexes
Description	During nuclear surveillance in yeast, the RNA exosome functions together with the TRAMP complexes. These include the DEAH-box RNA helicase Mtr4 together with an RNA-binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions for TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, binding specificity was apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association showed coenrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. We compared binding sites of TRAMP components with multiple nuclear RNA binding proteins, revealing preferential colocalization of subsets of factors. TRF5 deletion reduced Mtr4 recruitment and increased RNA abundance for mRNAs specifically showing high Trf5 binding.
HostingRepository	PRIDE
AnnounceDate	2020-07-02
AnnouncementXML	Submission_2020-07-01_22:49:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Clementine Delan-Forino
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-15 02:29:33	ID requested
⏵ 1	2020-07-01 22:49:29	announced

Delan-Forino C, Spanos C, Rappsilber J, Tollervey D, Substrate specificity of the TRAMP nuclear surveillance complexes. Nat Commun, 11(1):3122(2020) [pubmed]

submitter keyword: Nuclear surveillance, TRAMP complexes, RNA-binding proteins, Trf4, Trf5

David Tollervey
contact affiliation	WCCB, University of Edinburgh
contact email	David.Tollervey@ed.ac.uk
lab head
Clementine Delan-Forino
contact affiliation	University of Edinburgh
contact email	clementine.delanforino@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017114
     1. Label: PRIDE project
     2. Name: Substrate Specificity of the TRAMP Nuclear Surveillance Complexes