Infrared PAR-CLIP v1

Crosslinking and immunoprecipitation (CLIP) protocol based on 4-thiouridine incorporation and sequencing to determine binding sites of RNA-binding proteins (RBPs). This protocol has been used for the manuscript "Control of immediate early gene expression by CPEB4 repressor complex-mediated mRNA degradation" by Poetz, Lebedeva et al. , Genome Biology 2022. Based on the following protocols. - easy CLIP Porter DF, Miao W, Yang X, Goda GA, Ji AL, Donohue LKH, Aleman MM, Dominguez D, Khavari PA. easyCLIP analysis of RNA-protein interactions incorporating absolute quantification. Nat Commun. 2021 Mar 10;12(1):1569. doi: 10.1038/s41467-021-21623-4. PMID: 33692367; PMCID: PMC7946914. - PAR-CLIP Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010 Apr 2;141(1):129-41. doi: 10.1016/j.cell.2010.03.009. PMID: 20371350; PMCID: PMC2861495. - iCLIP Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J, Ule J. iCLIP: protein-RNA interactions at nucleotide resolution. Methods. 2014 Feb;65(3):274-87. doi: 10.1016/j.ymeth.2013.10.011. Epub 2013 Oct 25. PMID: 24184352; PMCID: PMC3988997. How to analyze the data: - For the general pipeline to map CLIP-seq reads, see https://github.com/ohlerlab/clip_pipeline or https://github.com/slebedeva/CLIP_mapping. For specific pipeline to map the data from this protocol, look into - https://github.com/slebedeva/CPEB4_public. - For the Ohler lab tool to call CLIP peaks, see https://github.com/ohlerlab/omniCLIP or https://github.com/slebedeva/omniCLIP. - For the Ohler lab deep learning tool to predict RBP binding sites based on CLIP peaks see https://github.com/ohlerlab/DeepRiPe.