RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions

Abstract

RNA–protein complexes have emerged as central players in numerous key cellular processes with significant relevance in health and disease. To further deepen our knowledge of RNA-binding proteins (RBPs), multiple proteome-wide strategies have been developed to identify RBPs in different species leading to a large number of studies contributing experimentally identified as well as predicted RBP candidate catalogs. However, the rapid evolution of the field led to an accumulation of isolated datasets, hampering the access and comparison of their valuable content. Moreover, tools to link RBPs to cellular pathways and functions were lacking. Here, to facilitate the efficient screening of the RBP resources, we provide RBP2GO (https://RBP2GO.DKFZ.de), a comprehensive database of all currently available proteome-wide datasets for RBPs across 13 species from 53 studies including 105 datasets identifying altogether 22 552 RBP candidates. These are combined with the information on RBP interaction partners and on the related biological processes, molecular functions and cellular compartments. RBP2GO offers a user-friendly web interface with an RBP scoring system and powerful advanced search tools allowing forward and reverse searches connecting functions and RBPs to stimulate new research directions.

The SARS-CoV-2 RNA–protein interactome in infected human cells

“…The expanded SARS-CoV-2 RNA interactome encompassed 104 human proteins and included 13 SARS-CoV-2-encoded proteins. The vast majority of the human RNA interactome proteins (100 proteins, 96%) have been identified previously in system-wide studies aimed at capturing proteins that crosslink to RNA 36 (Supplementary Table 2). Comparing this expanded SARS-CoV-2 RNA interactome with the poly(A)-RNA interactome in Huh7 cells 37 , revealed high overlap between both datasets (69 proteins, 66%) ( Fig.…”

“…We selected four inhibitors that target components of our expanded RNA interactome: PPIA; ARP2; ATP1A1; and DDX3X. While DDX3X is a DEAD-box RNA helicase and canonical RNA-binding protein, PPIA, ARP2 and ATP1A1 are non-classical RNA binders that are nonetheless robustly detected among RNA-binding proteins in Huh7 cells 36,37,79 . In addition to Huh7 cells, we evaluated all inhibitors in Calu3 cells, a human lung epithelial cell line that is naturally susceptible to SARS-CoV-2 infection.…”

A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly

“…RNA-binding proteins are defined as proteins that bind to RNA (Baltimore and Huang, 1970;Castello et al, 2012;Baltz et al, 2012;Gerstberger et al, 2014;Caudron-Herger et al, 2019;Caudron-Herger et al, 2021). Most RNA-binding proteins are characterized by a modular domain structure and contain repeated RNA-binding domains (Lunde et al, 2007).…”

NAPRT Expression Regulation Mechanisms: Novel Functions Predicted by a Bioinformatics Approach

“…For the TFs and RBPs that presented a significant correlation with NAPRT expression, we used the TRRUST v.2 database (grnpedia.org/trrust/, accessed on 9 March 2021 [ 45 ]) and the RBP2GO database ( , accessed on 26 March 2021 [ 46 ]) to search for their target genes. The gene set enrichment analysis of the target genes of the experimentally validated miRNAs was performed with miRTarBase 6.0.…”

“…For that purpose, we used three sources, namely, the Human Protein Atlas [ 43 ] annotated transcription dataset ( , accessed on 4 January 2021); the list of TFs from the ChIP-seq Peaks from the ENCODE Project [ 48 ] ( , accessed on 4 January 2021, source data version: ENCODE 3 November 2018); and the human transcription factors catalogue from Lambert et al 2018 [ 49 ]. In the case of the RBPs, we used the dataset published on the RBP2GO database [ 46 ]. On the remaining analysis, all genes in the genome were used as the enrichment background.…”