CLIPdb: a CLIP-seq database for protein-RNA interactions

Abstract

BackgroundRNA-binding proteins (RBPs) play essential roles in gene expression regulation through their interactions with RNA transcripts, including coding, canonical non-coding and long non-coding RNAs. Large amounts of crosslinking immunoprecipitation (CLIP)-seq data (including HITS-CLIP, PAR-CLIP, and iCLIP) have been recently produced to reveal transcriptome-wide binding sites of RBPs at the single-nucleotide level.DescriptionHere, we constructed a database, CLIPdb, to describe RBP-RNA interactions based on 395 publicly available CLIP-seq data sets for 111 RBPs from four organisms: human, mouse, worm and yeast. We consistently annotated the CLIP-seq data sets and RBPs, and developed a user-friendly interface for rapid navigation of the CLIP-seq data. We applied a unified computational method to identify transcriptome-wide binding sites, making the binding sites directly comparable and the data available for integration across different CLIP-seq studies. The high-resolution binding sites of the RBPs can be visualized on the whole-genome scale using a browser. In addition, users can browse and download the identified binding sites of all profiled RBPs by querying genes of interest, including both protein coding genes and non-coding RNAs.ConclusionManually curated metadata and uniformly identified binding sites of publicly available CLIP-seq data sets will be a foundation for further integrative and comparative analyses. With maintained up-to-date data sets and improved functionality, CLIPdb (http://clipdb.ncrnalab.org) will be a valuable resource for improving the understanding of post-transcriptional regulatory networks.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1273-2) contains supplementary material, which is available to authorized users.

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells

“…To identify sites in Xist where specific protein interactions occur, we searched for proteins both previously identified as Xist partners in TSCs (34) and present in the CLIPdb protein crosslinking and immunoprecipitation database (35) and identified CELF1, PTBP1, TARDBP, FUS, and RBFOX2 (34,36,37). We also performed digestion-optimized RIP-seq experiments in TSCs to identify binding sites for HuR, another Xist-interacting protein (34).…”

Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure

“…LCP1 is structured, but it does not have as many contiguous helices as TPT1. In PARClip analyses, only the RNA-binding protein RCTB was found to interact with the LCP1 mRNA coding sequence, although AGO2, LIN28B, IGF2BP1 and MOV10 can interact with the UTRs (Yang et al 2015). Due to its extensive structure, we expect that posttranscriptional regulation is important for LCP1 function.…”

“…We also downloaded PARClip data for TPT1 and LCP1 from CLIP-db (Yang et al 2015). Splice sites were defined as in the UCSC gtf files for each transcript (Karolchik et al 2004 …”

The yeast noncoding RNA interaction network

“…However, unlike proteinprotein interaction data, no systematic manual curation of the published literature in this area has yet been undertaken. Recently, a few resources have gathered RNA interactions and made them available on the web, such as Clipdb (Yang et al 2015), NPinter (Hao et al 2016), RAIN (Junge et al 2017), and RAID (Yi et al 2017). An important issue that previously made it difficult for interaction databases to capture and organize ncRNA interactions was the lack of a single central resource providing unambiguous identifiers for each RNA molecule, and linking that identifier to the sequence of that RNA.…”