We developed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) to quantify protein-RNA interactions in the whole transcriptome. We described the details of the iCLIP method and presented it in a video. We showed that the cDNAs in iCLIP truncate at crosslink sites, and developed computational methods based on cDNAs-starts for analysis of iCLIP data. We wrote several reviews on the advances in CLIP technologies: the 2012 and 2018 review describing the core steps and the variant experimental methods of iCLIP, the 2018 computational review describing the approaches for data analysis and quality control, and together with great colleagues, a primer on CLIP and complementary methods. We recently published an improved iCLIP protocol, and methods to visualise CLIP data and to analyse enriched sequence motifs.
Analysis of CLIP sequencing data benefits from use of customised computational software, much of which is available as part of the Nextflow pipeline for CLIP analysis, and specialised software is available for rapid demultiplexing of complex multiplexed libraries, comparative visualisation of crosslinking profiles across RNAs, identification of the peaks of clustered protein-RNA crosslink sites, and identification of sequence motifs enriched around prominent crosslinks.
Moreover, iMaps provides a free CLIP analysis web platform and well-curated community database to facilitate studies of RNA regulatory networks across organisms, with a backend based on the Nextflow pipelines. It is applicable to the many variant protocols of CLIP (such as iCLIP, eCLIP, etc), and is designed with the aim to help researchers (both computational and non-) gain meaningful biological and biomedical insights from their own, as well as public, data. It can be used to analyse unpublished data in a secure manner, and to obtain public CLIP data in a well-annotated format, along with various forms of quality control, visualisation and comparison. We have also created a Slack workspace so that you can give feedback on the new platform and future developments. The workspace also has a channel to ask questions about CLIP generally, which are then collated on our Q&A CLIP Forum. We hope you find these resources useful & if you have any questions and suggestions, or wish to contribute and join forces, please do let us know!