PXD006098

PXD006098 is an original dataset announced via ProteomeXchange.

Title	Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition
Description	During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNAbound proteome. This protein constellation consists of many conserved RBPs, with additional embryo- and stage-specific mRNA interactors that likely reflect the dynamics of RNA-protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of RBPs in embryogenesis, we focused on hnRNP A1. iCLIP and subsequent mRNA reporter assays revealed a function for hnRNP A1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3’UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that hnRNP A1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-miR-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of hnRNP A1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA-protein interactions during vertebrate MZT and shows that hnRNP A1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.
HostingRepository	PRIDE
AnnounceDate	2017-03-27
AnnouncementXML	Submission_2017-04-10_01:33:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	F Butter
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-15 02:08:10	ID requested
1	2017-03-27 00:53:20	announced
⏵ 2	2017-04-10 01:33:03	announced	Updated publication reference for PubMed record(s): 28381614.

Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM, Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome Res, 27(7):1184-1194(2017) [pubmed]

curator keyword: Biological

submitter keyword: zebrafish, embryo

Falk Butter
contact affiliation	Institute of Molecular Biology Ackermannweg 4 55128 Mainz
contact email	f.butter@imb-mainz.de
lab head
F Butter
contact affiliation	Dept. of Proteomics and Signal Transduction
contact email	f.butter@imb-mainz.de
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/2017/03/PXD006098

PRIDE project URI

• PRIDE
  1. PXD006098
     1. Label: PRIDE project
     2. Name: Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition