PXD011518

PXD011518 is an original dataset announced via ProteomeXchange.

Title	Localization of functionally distinct CDC42 isoforms in neurons requires alternative 3'UTR usage
Description	The proper subcellular localization of RNAs and local translational regulation is crucial in highly compartmentalized cells, such as neurons. RNA localization is mediated by specific cis-regulatory elements usually found in mRNA 3'UTRs. Therefore, processes that generate alternative 3'UTRs – alternative splicing and polyadenylation – have the potential to diversify mRNA localization patterns in neurons. Here, we performed mapping of alternative 3'UTRs in neurites and soma isolated from mESC-derived neurons. Our analysis identified 593 genes with differentially localized 3'UTR isoforms. In particular, we have shown that two isoforms of Cdc42 gene with distinct functions in neuronal polarity are differentially localized between neurites and soma of mESC-derived and mouse primary cortical neurons, at both mRNA and protein level. Using reporter assays and 3'UTR swapping experiments, we have identified the role of alternative 3’UTRs and mRNA transport in differential localization of alternative CDC42 protein isoforms. Moreover, we used SILAC to identify isoform-specific Cdc42 3'UTR-bound proteome with potential role in Cdc42 localization and translation. Our analysis points to usage of alternative 3'UTR isoforms as a novel mechanism to provide for differential localization of functionally diverse alternative protein isoforms.
HostingRepository	PRIDE
AnnounceDate	2019-12-13
AnnouncementXML	Submission_2019-12-13_07:34:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Koshi Imami
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-30 02:37:27	ID requested
1	2018-12-07 04:27:10	announced
⏵ 2	2019-12-13 07:34:12	announced	2019-12-13: Updated publication reference for PubMed record(s): 30590745.

Ciolli Mattioli C, Rom A, Franke V, Imami K, Arrey G, Terne M, Woehler A, Akalin A, Ulitsky I, Chekulaeva M, Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments. Nucleic Acids Res, 47(5):2560-2573(2019) [pubmed]

curator keyword: Biological

submitter keyword: CDC42, isoforms, localization, SILAC

Matthias Selbach
contact affiliation	MDC
contact email	matthias.selbach@mdc-berlin.de
lab head
Koshi Imami
contact affiliation	MDC
contact email	liqerume2000@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011518
     1. Label: PRIDE project
     2. Name: Localization of functionally distinct CDC42 isoforms in neurons requires alternative 3'UTR usage