PXD016741

PXD016741 is an original dataset announced via ProteomeXchange.

Title	System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organisation and function of RNA-protein complexes
Description	Production, function, and turnover of mRNA are orchestrated by multi-subunit machineries that play a central role in gene expression. Within these molecular machines, interactions with the target mRNA are mediated by RNA-binding proteins (RBPs), and the accuracy and dynamics of these RNA-protein interactions are essential for their function. Here, we show that fission yeast whole cell poly(A)+ RNA-protein crosslinking data provides system-wide information on the organisation and function of the RNA-protein complexes. We evaluate relative enrichment of cellular RBPs on poly(A)+ RNA to identify interactors with high RNA9 binding activity and provide key information about the RNA-binding properties of large multi10 protein complexes, such as the mRNA 3’ end processing machinery (cleavage and polyadenylation factor, CPF) and the RNA exosome. We demonstrate that different functional modules within CPF differ in their ability to interact with RNA. Importantly, we reveal that CPF forms additional contacts with RNA via the Fip1 subunit of the polyadenylation module and two subunits of the nuclease module. In addition, our data highlights the central role of the RNA helicase Mtl1 in RNA degradation by the exosome as mutations in Mtl1 lead to 16 disengagement of the exosome from RNA. We examine how routes of substrate access to the complex are affected upon mutation of exosome subunits. Our results provide important insights into how different components of the exosome contribute to engagement of the complex with substrate RNA. Overall, our data uncover how multi-subunit cellular machineries interact with RNA, on a proteome-wide scale.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-08_17:45:34.936.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shabaz Mohammed
SpeciesList	scientific name: Schizosaccharomyces pombe OY26; NCBI TaxID: 649908;
ModificationList	carbamoylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-13 08:18:56	ID requested
⏵ 1	2021-09-08 17:45:35	announced

Kilchert C, Kecman T, Priest E, Hester S, Aydin E, Kus K, Rossbach O, Castello A, Mohammed S, Vasiljeva L, RNA interactome reveal insights into organization and function of RNA-protein complexes. Genome Res, 30(7):1012-1026(2020) [pubmed]

submitter keyword: RNA exosome complex

RNA interactome capture

RNA-binding proteins

RNA-protein crosslinking

ribonucleoprotein complexes

Lidia Vasilieva
contact affiliation	University of Oxford
contact email	lidia.vasilieva@bioch.ox.ac.uk
lab head
Shabaz Mohammed
contact affiliation	University of Oxford
contact email	shabaz.mohammed@bioch.ox.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016741
     1. Label: PRIDE project
     2. Name: System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organisation and function of RNA-protein complexes