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Argonaute CLIP defines a deregulated miR-122-bound transcriptome that correlates with patient survival in human liver cancer. Mol Cell 67: 400–410.e7. [ PMC free article] [ PubMed] [ Google Scholar] Choder, M. mRNA imprinting: additional level in the regulation of gene expression. Cell. Logist. 1, 37–40 (2011). Gerstberger, S., Hafner, M., Ascano, M. & Tuschl, T. Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. Adv. Exp. Med. Biol. 825, 1–55 (2014). Lee, F. C. Y. & Ule, J. Advances in CLIP technologies for studies of protein–RNA interactions. Mol. Cell 69, 354–369 (2018).

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Köster, T., Reichel, M. & Staiger, D. CLIP and RNA interactome studies to unravel genome-wide RNA–protein interactions in vivo in Arabidopsis thaliana. Methods 178, 63–71 (2020).Stražar, M., Žitnik, M., Zupan, B., Ule, J. & Curk, T. Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. Bioinformatics 32, 1527–1535 (2016). HITS-CLIP: Panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA 1: 266–286. [ PMC free article] [ PubMed] [ Google Scholar] Chen, C.-L. & Perrimon, N. Proximity-dependent labeling methods for proteomic profiling in living cells. Wiley Interdiscip. Rev. Dev. Biol. 6, e272 (2017).

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Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci 14: 452–458. [ PMC free article] [ PubMed] [ Google Scholar]Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010). By default, text in Google Sheets is set to overflow. So if you need to unwrap text, you would simply choose "Overflow" in the text wrapping options. Ule, J. et al. An RNA map predicting Nova-dependent splicing regulation. Nature 444, 580–586 (2006). Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol Cell 48: 760–770. [ PMC free article] [ PubMed] [ Google Scholar]

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More than 100 RNA modifications have been described; most affect the assembly of protein–RNA complexes and therefore should be integrated into studies of protein–RNA interactions. Interestingly, mutations of certain methyltransferases can stabilize covalently linked protein–RNA catalytic intermediates, thus enabling CLIP to be performed without the need for UV cross-linking, as has been done for m5C-miCLIP 207. Most methods to date have been developed for transcriptomic studies of m 6A, the type of modification that is most common in mRNAs, and these include variants of CLIP, such as m 6A-miCLIP, which employ antibodies that recognize m 6A-containing RNA 208. The success of such approaches critically depends on the quality of the antibodies recognizing the modification 209. Therefore, similar to studies of protein–RNA interactions, integration of data from complementary methods will be valuable to gain a full picture of RNA modifications and their roles in RNP assembly 202, 210. Rescuing Z + agrin splicing in Nova null mice restores synapse formation and unmasks a physiologic defect in motor neuron firing. Proc Natl Acad Sci 106: 3513–3518. [ PMC free article] [ PubMed] [ Google Scholar] In the image below you can see this demonstrated, where there are multiple list items inside the cell, and each of them is on a new line. Lessons from non-canonical splicing. Nat Rev Gen 17: 407–421. [ PMC free article] [ PubMed] [ Google Scholar] Pietrosanto, M., Mattei, E., Helmer-Citterich, M. & Ferrè, F. A novel method for the identification of conserved structural patterns in RNA: from small scale to high-throughput applications. Nucleic Acids Res. 44, 8600–8609 (2016).Xu, Q. et al. Enhanced crosslinking immunoprecipitation (eCLIP) method for efficient identification of protein-bound RNA in mouse testis. J. Vis. Exp. https://doi.org/10.3791/59681 (2019). It is common to have tried widening your columns before determining the need for wrapping text, so try narrowing the column that contains the text to be wrapped to force excess text onto a new line. Zhang, C. & Darnell, R. B. Mapping in vivo protein–RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 29, 607–614 (2011).

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Munschauer, M. et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature 561, 132–136 (2018). This study uses RAP-MS and CLIP maps in a complementary fashion to map the assembly of NORAD lncRNA into an RNP that links proteins involved in DNA replication or repair. Which of the following options will make the text in the cell extend beyond the cell limits when the cell(s) to the right are blank? The RNA modification landscape in human disease. RNA 23: 1754–1769. [ PMC free article] [ PubMed] [ Google Scholar] Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat Neurosci 19: 335–346. [ PMC free article] [ PubMed] [ Google Scholar] Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc 9: 1282–1291. [ PMC free article] [ PubMed] [ Google Scholar]Darnell, J. C. et al. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 146, 247–261 (2011). miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19–miR-106a interaction. Nat Chem Biol 11: 107–114. [ PubMed] [ Google Scholar]