Proteomics

Dataset Information

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CAPRI RNA binding proteins and domains in Drosophila and Humans

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Drosophila Melanogaster (fruit Fly)

TISSUE(S): Cell Culture

SUBMITTER: Amol Panhale  

LAB HEAD: Asifa Akhtar

PROVIDER: PXD013338 | Pride | 2019-07-02

REPOSITORIES: Pride

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Publications

CAPRI enables comparison of evolutionarily conserved RNA interacting regions.

Panhale Amol A   Richter Florian M FM   Ramírez Fidel F   Shvedunova Maria M   Manke Thomas T   Mittler Gerhard G   Akhtar Asifa A  

Nature communications 20190618 1

RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more  ...[more]