Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

EC Urdaneta, CH Vieira-Vieira, T Hick… - Nature …, 2019 - nature.com
Recent methodological advances allowed the identification of an increasing number of RNA-
binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however …

Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach

BP Tsai, X Wang, L Huang, ML Waterman - Molecular & Cellular Proteomics, 2011 - ASBMB
Identification of proteins in RNA-protein complexes is an important step toward
understanding regulation of RNA-based processes. Because of the lack of appropriate …

RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins

TS Stenum, AD Kumar, FA Sandbaumhüter… - Nucleic Acids …, 2023 - academic.oup.com
RNA-binding proteins (RPBs) are deeply involved in fundamental cellular processes in
bacteria and are vital for their survival. Despite this, few studies have so far been dedicated …

Genetically encoded chemical crosslinking of RNA in vivo

W Sun, N Wang, H Liu, B Yu, L Jin, X Ren, Y Shen… - Nature …, 2023 - nature.com
Protein–RNA interactions regulate RNA fate and function, and defects can lead to various
disorders. Such interactions have mainly been studied by nucleoside-based UV crosslinking …

CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo

Z Wang, J Tollervey, M Briese, D Turner, J Ule - Methods, 2009 - Elsevier
UV cross-linking and immunoprecipitation assay (CLIP) can identify direct interaction sites
between RNA-binding proteins and RNAs in vivo, and has been used to study several …

Defining the RNA interactome by total RNA‐associated protein purification

V Shchepachev, S Bresson, C Spanos… - Molecular systems …, 2019 - embopress.org
The RNA binding proteome (RBP ome) was previously investigated using UV crosslinking
and purification of poly (A)‐associated proteins. However, most cellular transcripts are not …

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

RML Queiroz, T Smith, E Villanueva… - Nature …, 2019 - nature.com
Existing high-throughput methods to identify RNA-binding proteins (RBPs) are based on
capture of polyadenylated RNAs and cannot recover proteins that interact with …

Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs

DM Ribeiro, A Zanzoni, A Cipriano… - Nucleic acids …, 2018 - academic.oup.com
The human transcriptome contains thousands of long non-coding RNAs (lncRNAs).
Characterizing their function is a current challenge. An emerging concept is that lncRNAs …

RAP-MS: a method to identify proteins that interact directly with a specific RNA molecule in cells

CA McHugh, M Guttman - RNA detection: Methods and protocols, 2018 - Springer
RNA molecules interact with proteins to perform a variety of functions in living cells. The
binding partners of many RNAs, in particular the newly discovered class of long noncoding …

System-wide identification of RNA-binding proteins by interactome capture

A Castello, R Horos, C Strein, B Fischer… - Nature protocols, 2013 - nature.com
Owing to their preeminent biological functions, the repertoire of expressed RNA-binding
proteins (RBPs) and their activity states are highly informative about cellular systems. We …