PXD004193

PXD004193 is an original dataset announced via ProteomeXchange.

Title	A compendium of RNA-binding proteins that regulate microRNA biogenesis
Description	During microRNA-biogenesis, stem-loop structured precursors are processed in two endonucleolytic steps, giving rise to mature microRNAs (miRNAs). This process is not only regulated at the level of transcription but also posttranscriptionally by RNA-binding proteins (RBPs). Here we have used a proteomics-based pull-down approach to map and characterize the interactome of 72 pre-miRNAs in eleven cell lines. We identify over 150 RBPs that interact specifically with distinct pre-miRNAs. To demonstrate their functional relevance, we used RNAi knockdown and CRISPR/Cas-mediated knockout experiments and analyzed changes in miRNA levels. Indeed, a large number of the investigated candidates have effects on miRNA-processing under our experimental conditions, including several C3H-zinc-finger proteins. Ultimately, we show that TRIM71/Lin41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. In summary, we provide an extended database of RBPs that interact with pre-miRNAs in different cell types helping to elucidate posttranscriptional regulation of miRNA biogenesis on a global scale.
HostingRepository	PRIDE
AnnounceDate	2019-11-08
AnnouncementXML	Submission_2019-11-08_00:44:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kuan-Ting Pan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-23 00:16:05	ID requested
1	2017-04-26 13:46:36	announced
⏵ 2	2019-11-08 00:44:07	announced	2019-11-08: Updated publication reference for PubMed record(s): 31665645, 28431233.

Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Rep, 29(5):1351-1368.e5(2019) [pubmed]

Treiber T, Treiber N, Plessmann U, Harlander S, Dai, ß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G, A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Mol Cell, 66(2):270-284.e13(2017) [pubmed]

curator keyword: Biological

submitter keyword: RNA-protein interaction, microRNA, Mass Spectrometry

Henning Urlaub
contact affiliation	1. Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany 2. Bioanalytics, University Medical Center, Robert-Koch-Straße 40, 37075 Göttingen, Germany
contact email	henning.urlaub@mpibpc.mpg.de
lab head
Kuan-Ting Pan
contact affiliation	MPI for Biophysical Chemistry
contact email	kpan@mpibpc.mpg.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/2017/04/PXD004193

PRIDE project URI

• PRIDE
  1. PXD004193
     1. Label: PRIDE project
     2. Name: A compendium of RNA-binding proteins that regulate microRNA biogenesis