References

Chakrabarti, A.M., Haberman, N., Praznik, A., Luscombe, N.M., and Ule, J. (2018). Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies. Annu. Rev. Biomed. Data Sci. 1, 235–261.arrow-up-right

Chen, X., Castro, S.A., Liu, Q., Hu, W., and Zhang, S. (2019). Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. Methods 155, 49–57.arrow-up-right

De, S., and Gorospe, M. (2017). Bioinformatic tools for analysis of CLIP ribonucleoprotein data. Wiley Interdiscip. Rev. RNA 8.arrow-up-right

Erika C Urdanetabenedikt (2020). Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Methods 178, 72–82.arrow-up-right

Garzia, A., Meyer, C., Morozov, P., Sajek, M., and Tuschl, T. (2017). Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins. Methods 118-119, 24–40.arrow-up-right

Haberman, N., Huppertz, I., Attig, J., König, J., Wang, Z., Hauer, C., Hentze, M.W., Kulozik, A.E., Le Hir, H., Curk, T., et al. (2017). Insights into the design and interpretation of iCLIP experiments. Genome Biol. 18.arrow-up-right

König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D.J., Luscombe, N.M., and Ule, J. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915.arrow-up-right

Lee, F.C.Y., and Ule, J. (2018). Advances in CLIP Technologies for Studies of Protein-RNA Interactions. Mol. Cell 69, 354–369.arrow-up-right

McIntyre, A.B.R., Gokhale, N.S., Cerchietti, L., and Jaffrey, S.R. (2019). Limits in the detection of m6A changes using MeRIP/m6A-seq. BioRxiv.arrow-up-right

Moore, K.S., and AC’t Hoen, P. (2019). Computational approaches for the analysis of RNA–protein interactions: A primer for biologists. J. Biol. Chem.arrow-up-right

Schwartz, S. (2018). m1A within cytoplasmic mRNAs at single nucleotide resolution: a reconciled transcriptome-wide map. RNA 24, 1427–1436.arrow-up-right

Smith, T., Heger, A., and Sudbery, I. (2017). UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 27, 491–499.arrow-up-right

Ule, J., Jensen, K., Mele, A., and Darnell, R.B. (2005). CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37, 376–386.arrow-up-right

Ule, J., Hwang, H.-W., and Darnell, R.B. (2018). The Future of Cross-Linking and Immunoprecipitation (CLIP). Cold Spring Harb. Perspect. Biol. 10.arrow-up-right

Wang, L.K., and Shuman, S. (2002). Mutational analysis defines the 5’-kinase and 3'-phosphatase active sites of T4 polynucleotide kinase. Nucleic Acids Res. 30, 1073–1080.arrow-up-rightWheeler, E.C., Van Nostrand, E.L., and Yeo, G.W. (2018). Advances and challenges in the detection of transcriptome-wide protein-RNA interactions. Wiley Interdiscip. Rev. RNA 9.arrow-up-right

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