PXD004640-3

PXD004640 is an original dataset announced via ProteomeXchange.

Title	RNA localization is a key determinant of neurite-enriched proteome
Description	RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells. Our results reveal mRNA localization as a key determinant of protein localization to neurites that accounts for around a half of the neurite-localized proteome. Moreover, we identify non-coding RNAs and RNA-binding proteins targeted to neurites.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:31:45.493.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	acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-07-22 07:27:41	ID requested
1	2018-06-06 04:37:40	announced
2	2019-12-13 07:37:14	announced	2019-12-13: Updated publication reference for PubMed record(s): 28928394, 30590745.
⏵ 3	2024-10-22 04:31:56	announced	2024-10-22: Updated project metadata.

Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, M, ü, ller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M, RNA localization is a key determinant of neurite-enriched proteome. Nat Commun, 8(1):583(2017) [pubmed]

10.1038/s41467-017-00690-6;

10.1093/nar/gky1270;

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: Mouse ES, local translation, differentiation, LFQ, LC-MS/MS

Matthias Selbach
contact affiliation	Max Delbrück Center for Molecular Medicine in the Helmholtz Association
contact email	matthias.selbach@mdc-berlin.de
lab head
Koshi Imami
contact affiliation	Kyoto University
contact email	liqerume2000@gmail.com
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/2018/06/PXD004640

PRIDE project URI

• PRIDE
  1. PXD004640
     1. Label: PRIDE project
     2. Name: RNA localization is a key determinant of neurite-enriched proteome