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.
CLIP Q&A and Forum
We established a Q&A and forum to discuss the experimental and computational questions arising about CLIP and its variants.
Many computational tools have been developed for analysis of data produced by CLIP and its variant protocols, as described in our review. In collaboration with Tomaz Curk, we developed iCount, a Python code that, among others, defines the peaks of clustered protein-RNA crosslink sites. We also collaborate with the Luscombe lab, which recently released the Nextflow pipeline for CLIP analysis, which makes the code easily accessible so that users can comment or contribute to the pipeline itself.
Moreover, we have been working with colleagues over the years to establish a free CLIP analysis web platform and well-curated community database to facilitate studies of RNA regulatory networks across organisms. A prototype platform, iMaps v1, has been available since 2019 and will be operational till end of September 2021. 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 It can be used to analyse unpublished data in a secure manner, and to obtain public CLIP data in a well-annotated format, along with various forms of quality control, visualisation and comparison.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 are currently developing iMaps v2, which will have several improvements, including a backend based on Nextflow. 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!
Nextflow pipeline and iMAPs web platform
iMaps web platform and associated Nextflow CLIP analysis pipeline