The role of 3' UTR variation in the molecular pathogenesis of motor neuron disease (360G-Wellcome-103760_Z_14_A)

UV cross-linking and immunoprecipitation (CLIP) is a commonly used method to profile endogenous protein-RNA interactions by sequencing RNA fragments that copurify with a selected RNA-binding protein (RBPs). Integrative analysis of available CLIP data is hampered by the lack of a unified CLIP data resource. 27 variants of the method have already been developed, and these have been used in over a hundred labs to produce thousands of data sets for several hundred RBPs in diverse species, from bacteria to human (Lee and Ule, 2018). Moreover, many tools exist for integrative analysis of processed CLIP data, but unfortunately, there is no available data repository that would provide a unified processing of various types of CLIP data produced by different groups. Here, we propose to establish a public repository of all public CLIP data produced in different cell types, tissues and species. Such a resource would empower wet lab biologists to explore processed CLIP data in a user-friendly manner, and to assess if variations between different CLIP protocols produced in different laboratories influence the reproducibility, technical artefacts and other measures of data quality. Moreover, a unified analysis platforms will provide consistently comparable data to bioinformaticians for integrative meta-analyses of all available data from the various groups. This would enhance the capacity of the RNA community to advance our understanding of epitranscriptomics, and of the regulatory mechanisms of protein-RNA complexes that regulate gene expression. Lee, F.C.Y., and Ule, J. (2018). Advances in CLIP Technologies for Studies of Protein-RNA Interactions. Mol. Cell 69, 354–369.