Protein–RNA interactions: new genomic technologies and perspectives

J König, K Zarnack, NM Luscombe, J Ule - Nature Reviews Genetics, 2012 - nature.com
RNA-binding proteins are key players in the regulation of gene expression. In this Progress
article, we discuss state-of-the-art technologies that can be used to study individual RNA …

Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays

SA Tenenbaum, PJ Lager, CC Carson, JD Keene - Methods, 2002 - Elsevier
Although in vitro methods have been used to identify putative targets of mRNA-binding
proteins, direct in vivo methods are needed to identify endogenously associated mRNAs …

RNA localization signals: deciphering the message with bioinformatics

RS Hamilton, I Davis - Seminars in cell & developmental biology, 2007 - Elsevier
mRNA localization is an important posttranscriptional method of targeting proteins to their
site of function. The sorting of transcripts to their correct intracellular destination is achieved …

RBPmap: a web server for mapping binding sites of RNA-binding proteins

I Paz, I Kosti, M Ares Jr, M Cline… - Nucleic acids …, 2014 - academic.oup.com
Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs)
that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via …

RNA-centric approaches to study RNA-protein interactions in vitro and in silico

A Dasti, F Cid-Samper, E Bechara, GG Tartaglia - Methods, 2020 - Elsevier
Given their central role in translation, splicing, localization and stability of transcripts, RNA
binding proteins (RBPs) are key regulators of several cellular processes. While experimental …

Circuitry of mRNA regulation

A Kanitz, AP Gerber - Wiley Interdisciplinary Reviews: Systems …, 2010 - Wiley Online Library
Some of the classical paradigms of gene regulation have been challenged by global‐scale
analysis of eukaryotic transcriptional and post‐transcriptional gene regulation (PTGR), made …

Experimental and computational considerations in the study of RNA-binding protein-RNA interactions

EL Van Nostrand, SC Huelga, GW Yeo - RNA Processing: Disease and …, 2016 - Springer
After an RNA is transcribed, it undergoes a variety of processing steps that can change the
encoded protein sequence (through alternative splicing and RNA editing), regulate the …

Towards deciphering the principles underlying an mRNA recognition code

A Serganov, DJ Patel - Current opinion in structural biology, 2008 - Elsevier
Messenger RNAs interact with a number of different molecules that determine the fate of
each transcript and contribute to the overall pattern of gene expression. These interactions …

New sequencing methodologies reveal interplay between multiple RNA-binding proteins and their RNAs

S Melamed - Current genetics, 2020 - Springer
It is now established that base-pairing regulatory RNAs are key players in post-
transcriptional regulatory networks where they affect the translation and/or stability of their …

Structural and functional features of eukaryotic mRNA untranslated regions

G Pesole, F Mignone, C Gissi, G Grillo, F Licciulli… - Gene, 2001 - Elsevier
The crucial role of the non-coding portion of genomes is now widely acknowledged. In
particular, mRNA untranslated regions are involved in many post-transcriptional regulatory …