PXD030419

PXD030419 is an original dataset announced via ProteomeXchange.

Title	Comparative analyses of vertebrate CPEB-family of proteins define two sub-families with distinct, but coordinated, functions in post-transcriptional regulation of gene expression
Description	Background: The vertebrate CPEB-family of RNA-binding proteins promote translational repression or activation of their target mRNAs, which harbor cytoplasmic polyadenylation elements (CPEs) in their 3’ UTRs, through cytoplasmic changes in their poly(A) tail lengths. However, their regulation(s) and mechanism(s) of action have not been systematically addressed as a family. Results: Here we perform a comparative analysis of the four vertebrate CPEBs in their regulation by phosphorylation, supramolecular assemblies’ composition and properties and in their mRNA targets. Conclusions: We show that although all four CPEBs are able to recruit CCR4-NOT deadenylation complex when not phosphorylated, their mechanisms of action determine two subfamilies with distinct, but coordinated, regulation by phosphorylation and target specificity. Thus, CPEB1 forms ribonucleoprotein complexes that are remodeled upon a single phosphorylation event, by AurkA, and are associated with mRNAs containing canonical CPEs. On the other hand, CPEB2-4 are regulated by multiple proline-directed phosphorylations that control their liquid-liquid phase-separation. CPEB2-4 mRNA-targets include CPEB1-bound transcripts, with canonical CPEs, but also a specific subset of mRNAs with non-canonical CPEs. In turn, CPEB2-4 coacervates display compositional, morphological and dynamic differences. Altogether, these results show how, globally, the CPEB family of proteins is able to integrate cellular cues to generate a finetuned adaptive response in gene expression regulation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:24:16.074.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marina Gay
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-15 05:39:35	ID requested
1	2022-10-05 07:22:44	announced
⏵ 2	2023-11-14 08:24:18	announced	2023-11-14: Updated project metadata.

Duran-Arqu, é B, Ca, ñ, ete M, Castellazzi CL, Bartomeu A, Ferrer-Caelles A, Reina O, Caball, é A, Gay M, Arauz-Garofalo G, Belloc E, Mendez R, Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation. Genome Biol, 23(1):192(2022) [pubmed]

submitter keyword: mRNA translation, deadenylation, CPEB, phosphorylation, CCR4-NOT complex, phase-separation, BioID, 3’UTR

Raul Mendez
contact affiliation	Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
contact email	raul.mendez@irbbarcelona.org
lab head
Marina Gay
contact affiliation	Institute for Research in Biomedicine
contact email	marina.gay@irbbarcelona.org
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/10/PXD030419

PRIDE project URI

• PRIDE
  1. PXD030419
     1. Label: PRIDE project
     2. Name: Comparative analyses of vertebrate CPEB-family of proteins define two sub-families with distinct, but coordinated, functions in post-transcriptional regulation of gene expression