Moore, M. J. et al. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat. Protoc. 9, 263–293 (2014). Kido, K. et al. AirID, a novel proximity biotinylation enzyme, for analysis of protein–protein interactions. eLife 9, e54983 (2020).

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Rot, G. et al. High-resolution RNA maps suggest common principles of splicing and polyadenylation regulation by TDP-43. Cell Rep. 19, 1056–1067 (2017). Slobodin, B. & Gerst, J. E. A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes. RNA 16, 2277–2290 (2010). Keep collections to yourself or inspire other shoppers! Keep in mind that anyone can view public collections - they may also appear in recommendations and other places.Nabeel-Shah, S. et al. SARS-CoV-2 nucleocapsid protein attenuates stress granule formation and alters gene expression via direct interaction with host mRNAs. Cold Spring Harb. Lab. https://doi.org/10.1101/2020.10.23.342113 (2020). For example, if you want to put a list of items inside a single cell, type the first item, then press Ctrl + Enter on the keyboard, type the second item, and repeat as many times as you want. To unwrap the text for this example, we simply select column B, and then select "Overflow" from the text wrapping options. Proximity-CLIP 11 and the related technique APEX-seq 45, 46, 47 allow the determination of RNA distribution to specific subcellular locations. Both techniques rely on the biotinylation of RNAs (exploited in APEX-seq) and proteins (exploited in Proximity-CLIP) by the engineered ascorbic acid peroxidase protein APEX2 (ref. 48), a tool widely used to quantify the localized proteome 49 (Supplementary Table 1). To allow subcellular compartment-specific biotinylation of RNA and proteins, APEX2 is typically fused to specific localization elements 50. In the case of Proximity-CLIP, prior to protein biotinylation, nascent transcripts are labelled with either 4SU or 6SG and cross-linked to interacting RBPs with UV light of 312–365 nm (Fig. 2a). The compartment-specific proteome, including cross-linked RNPs, is then isolated on streptavidin beads and cross-linked RNA fragments are isolated and sequenced following mild RNase digestion. The characteristic mutations in the cDNA resulting from the use of photoreactive nucleosides reveal cross-linked sequences. A distinctive feature of Proximity-CLIP is that the sequencing of RBP-protected footprints allows for both the profiling of localized RNAs and the identification of protein-occupied, possibly regulatory, cis-acting elements on RNA. In contrast to APEX-seq, this approach provides a snapshot of regulatory elements on RNA that are occupied in the examined compartments.

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If you want to decide where the lines break (where they go to a new line) in your Google spreadsheet, then you can manually wrap text by inserting a new line inside the cell, exactly where you want it. Bahrami-Samani, E., Penalva, L. O. F., Smith, A. D. & Uren, P. J. Leveraging cross-link modification events in CLIP-seq for motif discovery. Nucleic Acids Res. 43, 95–103 (2015). Attig, J. et al. Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing. Cell 174, 1067–1081.e17 (2018).Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017). A crucial step in understanding RNA-related gene regulation and its relationship to disease is identifying how RNAs are bound and hence regulated by RNA-binding proteins (RBPs) in specific cell types and subcellular compartments. Driving our interest in this topic has been the growing list of human neurologic diseases that have RNA dysregulation at their core ( Conlon and Manley 2017). The first method developed for this purpose used antibodies against the spliceosomal Sm proteins (lupus autoimmune sera) to identify the small nuclear RNAs (snRNAs), which interact with Sm proteins within the abundant small nuclear ribonucleoprotein complexes (snRNPs) ( Lerner and Steitz 1979). This method, later referred to as RIP (RNP/RNA immunoprecipitation), relies on immunoprecipitation (IP) of an RBP under conditions that preserve RNPs ( Niranjanakumari et al. 2002). However, RIP can suffer from low specificity, partly because it preserves protein–protein interactions and can therefore purify multiple RBPs in complex with their bound RNAs, and partly because RNA–protein complexes can reassociate in vitro ( Mili and Steitz 2004). Zhu, Y. et al. POSTAR2: deciphering the post-transcriptional regulatory logics. Nucleic Acids Res. 47, D203–D211 (2019).