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Tauber, D., Tauber, G. & Parker, R. Mechanisms and regulation of RNA condensation in RNP granule formation. Trends Biochem. Sci. 45, 764–778 (2020). Investigating the RNP composition in higher plants is made difficult by several technical challenges. In contrast to mammalian cell cultures, plant cell cultures cannot be cultivated in monolayers and are of limited use for CLIP techniques; as a result, experiments have mostly been performed in transgenic Arabidopsis plants expressing epitope-tagged RBPs 17, 18. Although the presence of UV-absorbing pigments and secondary metabolites such as chlorophyll and flavonoids can inhibit cross-linking efficiency, UVC-based cross-linking has been successfully applied to whole plants 17, 18. Another obstacle in plants is the rigid cell wall that requires mechanical force and harsh denaturing conditions for efficient cell lysis 137. Moreover, the large amounts of endogenous RNases present in the plant vacuole require the use of RNase inhibitors to prevent extensive RNA degradation during extract preparation (also reported for pancreatic tissue). To ensure a controlled RNase treatment to fragment RNA, RNase treatment is performed after immunoprecipitation of the RNA–protein complexes rather than on the lysate 18. Huppertz, I. et al. iCLIP: protein–RNA interactions at nucleotide resolution. Methods 65, 274–287 (2014).

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Kapusta, A. & Feschotte, C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet. 30, 439–452 (2014). Mellacheruvu, D. et al. The CRAPome: a contaminant repository for affinity purification–mass spectrometry data. Nat. Methods 10, 730–736 (2013). Sibley, C. R., Blazquez, L. & Ule, J. Lessons from non-canonical splicing. Nat. Rev. Genet. 17, 407–421 (2016). Casas-Vila, N., Sayols, S., Pérez-Martínez, L., Scheibe, M. & Butter, F. The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae. Nat. Commun. 11, 2789 (2020). If your column is too narrow when using text wrapping, your row height may become too tall. So when you have lots of text… it can be helpful to anticipate the need for more space and adjusting the column before applying "Wrap".Goering, R. et al. FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences. eLife 9, e52621 (2020). Ellington, A. D. & Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990). Li, Y., Aggarwal, M. B., Ke, K., Nguyen, K. & Spitale, R. C. Improved analysis of RNA localization by spatially restricted oxidation of RNA–protein complexes. Biochemistry 57, 1577–1581 (2018). Read about the NEB’s set of protein tools for the specific labeling (SNAP-, CLIP-, ACP- and MCP-tags) of fusion proteins.

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The first aspect that has been varied in the CLIP methods is the cross-linking of protein–RNA complexes. Most variants of CLIP expose cells or tissues to the UVC wavelength (254 nm), a procedure that usually takes less than a minute with cells placed on ice ( Ule et al. 2003) or frozen in liquid nitrogen. Photoactivatable ribonucleoside-enhanced (PAR)-CLIP introduces a variation in the cross-linking strategy ( Hafner et al. 2010), in which live cells are preincubated for hours with PARs4-thiouridine (4SU) or 6-thioguanosine (6SG), which label the RNA in vivo and enable protein–RNA cross-linking to be performed with UVA wavelength (365 nm). A mass spectrometry study has compared this protocol with UVC cross-linking to conclude that the efficiency of the two approaches is quite similar across all RBPs ( Castello et al. 2012). The advantage of UVA cross-linking is its decreased capacity to induce DNA damage as compared with UVC, although in most CLIP experiments samples are chilled or frozen during ∼30-sec-long UV cross-linking and then immediately solubilized, so that biologic consequences of DNA damage are minimal. The disadvantages of PAR-CLIP are its limitation to biological systems in which the photoactivatable nucleosides can be efficiently incorporated, and its recommended use of >100 million cells ( Danan et al. 2016), whereas one million or less are used by standard variants of CLIP. Moreover, prolonged preincubation with 6SG or 4SU can cause cellular toxicity, including stress responses and inhibition of ribosomal RNA (rRNA) synthesis ( Burge Warner, J. R. & McIntosh, K. B. How common are extraribosomal functions of ribosomal proteins? Mol. Cell 34, 3–11 (2009). Gerstberger, S., Hafner, M. & Tuschl, T. A census of human RNA-binding proteins. Nat. Rev. Genet. 15, 829–845 (2014). Darnell, J. C. et al. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 146, 247–261 (2011).In column C, you can see that the notes which were typed, are too long to fit inside the cells. Since there is not data to the right of the notes in column C, the text is overflowing into the next cells (more on this later). Column Manager: Add a Specific Number of Columns | Move Columns | Toggle Visibility Status of Hidden Columns | Compare Ranges & Columns...

Cross-Linking and Immunoprecipitation (CLIP) The Future of Cross-Linking and Immunoprecipitation (CLIP)

Miniard, A. C., Middleton, L. M., Budiman, M. E., Gerber, C. A. & Driscoll, D. M. Nucleolin binds to a subset of selenoprotein mRNAs and regulates their expression. Nucleic Acids Res. 38, 4807–4820 (2010). Haberman, N. et al. Insights into the design and interpretation of iCLIP experiments. Genome Biol. 18, 7 (2017). Mark your USB cables so you don't lose them anymore - Original gift idea - clip for all types of cables - fixed with 2 screws so reusable Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia

Zhang, Y. et al. Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation. Cell Res. 25, 864–876 (2015). Lin, C. & Miles, W. O. Beyond CLIP: advances and opportunities to measure RBP–RNA and RNA–RNA interactions. Nucleic Acids Res. 47, 5490–5501 (2019). Mili, S. & Steitz, J. A. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 10, 1692–1694 (2004).