PXD013338

PXD013338 is an original dataset announced via ProteomeXchange.

Title	CAPRI RNA binding proteins and domains in Drosophila and Humans
Description	In the current work, we present a comprehensive coverage of the RNA-binding protein (RBP) interactome of Drosophila at four levels of resolution. The highest level tackled in our study represents the RNA-protein complexes, which we address by combining formaldehyde crosslinking of Drosophila S2 cells followed by polyA+ pulldown using oligo-dT beads. On the second level of resolution we identified direct RBPs in the cell using UV crosslinking. Given the paucity of information available on the RNA-binding regions in the Drosophila RBPs that we uncovered, we developed the CAPRI methodology to dissect RNA binding domains (RBDs) on a systematic level. The CAPRI technique provided the final two levels of resolution of our study. The protocol utilised FASP to enable isolation of peptides crosslinked to RNA and peptides adjacent to these crosslinked sites. The CAPRI pipeline mapped both the peptides in proximity to RNA and the precise amino acids contacting RNA. The RNA crosslinked peptide analysis was made by de novo peptide analysis software, PEAKS (Bioinformatics Solutions Inc). In a separate analysis, we also applied FA crosslinking to RBD capture and showed it to be a viable complementary method to the CAPRI workflow. We next applied CAPRI interactome capture to human cells in order to analyse the evolutionary conservation of newly identified RNA binding domains between the two species. These interactome capture techniques and the datasets acquired using them are discussed in detail in the following sections. In summary, we present a comprehensive resource for the study of RNA-protein interactions at a high throughput scale.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_03:58:37.742.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amol Panhale
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-02 01:00:59	ID requested
1	2019-07-02 06:20:00	announced
⏵ 2	2024-10-22 03:58:46	announced	2024-10-22: Updated project metadata.

10.1038/s41467-019-10585-3;

Panhale A, Richter FM, Ram, í, rez F, Shvedunova M, Manke T, Mittler G, Akhtar A, CAPRI enables comparison of evolutionarily conserved RNA interacting regions. Nat Commun, 10(1):2682(2019) [pubmed]

curator keyword: Biological

submitter keyword: RNA crosslinked peptides, RNA protein interaction

Asifa Akhtar
contact affiliation	Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg im Breisgau, Germany
contact email	akhtar@ie-freiburg.mpg.de
lab head
Amol Panhale
contact affiliation	Max Planck Institute of Immunobiology and Epigenetics
contact email	panhale@ie-freiburg.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/2019/07/PXD013338

PRIDE project URI

• PRIDE
  1. PXD013338
     1. Label: PRIDE project
     2. Name: CAPRI RNA binding proteins and domains in Drosophila and Humans