CLIP: a method for identifying protein-RNA interaction sites in living cells.

By Jernej Ule, K. Jensen, Aldo Mele, R. Darnell. Methods, 2005

630 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2f02e3c59d9a653227f0ccc71a5ccb088e0214ec

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In Molecular Biology

Citations in the corpus

miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database (2019, background): “In addition, this updated version has integrated additional 100 CLIP-seq data from nine independent studies that can be used to support many MTIs (Supplementary Table S1).”
Revealing protein–lncRNA interaction (2015, methodology): “The Cross-Linking ImmunoPrecipitation (CLIP) [59] procedure takes advantage of the ability of 254 nm ultraviolet (UV) light to induce the in vivo formation of covalent bonds between”
Molecular Interplay of the Non-coding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a (2010, methodology): “CLIP was performed using a previously established procedure (Ule et al., 2005) with modifications.”
RNA‐binding proteins and post‐transcriptional gene regulation (2008, positive): “Recently, this method has been adapted, using tagged proteins and including an immunoprecipitation step following cross-linking (cross-linking and immunoprecipitation or CLIP) [17].”
ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs (2011, neutral): “In Vivo Cross-Linking and ImmunoPrecipitation (CLIP) Assay CLIP analyses of methylated and unmethylated Pc2 were performed as previously described (Ule et al., 2005).”
A large intergenic non-coding RNA induced by p53 mediates global gene repression in the p53 response (2010, methodology): “We further performed analogous RIP experiments with formaldehyde crosslinked cells followed by stringent washing conditions (Ule et al., 2005) to rule out potential nonspecific interactions.”
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (2011, background): “Nuclease signature in the CLIP reads Another difference between CLIP protocols is that protein-bound RNAs are fragmented through partial digestion with a mixture of RNase T1 and RNase”