Engineering RNA‐binding proteins with diverse activities

H Wei, Z Wang - Wiley Interdisciplinary Reviews: RNA, 2015 - Wiley Online Library
With generations of efforts to understand RNA functions in diverse cellular processes, RNA‐
binding proteins (RBPs) have emerged to be one of the central players in regulating RNA …

Deciphering the protein‐RNA recognition code: Combining large‐scale quantitative methods with structural biology

J Hennig, M Sattler - Bioessays, 2015 - Wiley Online Library
RNA binding proteins (RBPs) are key factors for the regulation of gene expression by
binding to cis elements, ie short sequence motifs in RNAs. Recent studies demonstrate that …

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

S Sohrabi-Jahromi, J Söding - Bioinformatics, 2021 - academic.oup.com
Motivation Understanding how proteins recognize their RNA targets is essential to elucidate
regulatory processes in the cell. Many RNA-binding proteins (RBPs) form complexes or …

[HTML][HTML] RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites

J Luo, L Liu, S Venkateswaran, Q Song, X Zhou - Scientific reports, 2017 - nature.com
RNA and protein interactions play crucial roles in multiple biological processes, while these
interactions are significantly influenced by the structures and sequences of protein and RNA …

[HTML][HTML] Compendium of methods to uncover RNA-protein interactions in vivo

M Majumder, V Palanisamy - Methods and Protocols, 2021 - mdpi.com
Control of gene expression is critical in shaping the pro-and eukaryotic organisms' genotype
and phenotype. The gene expression regulatory pathways solely rely on protein–protein …

A rapid method for assessing the RNA-binding potential of a protein

K Bendak, FE Loughlin, V Cheung… - Nucleic acids …, 2012 - academic.oup.com
In recent years, evidence has emerged for the existence of many diverse types of RNA,
which play roles in a wide range of biological processes in all kingdoms of life. These …

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 …

Revealing protein–lncRNA interaction

F Ferre, A Colantoni… - Briefings in …, 2016 - academic.oup.com
Long non-coding RNAs (lncRNAs) are associated to a plethora of cellular functions, most of
which require the interaction with one or more RNA-binding proteins (RBPs); similarly, RBPs …

Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale

J Gong, Y Ju, D Shao, QC Zhang - Quantitative Biology, 2018 - Springer
Background RNA molecules play crucial roles in various biological processes. Their
regulation and function are mediated by interacting with other molecules. Among them RNA …

A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data

M Polishchuk, I Paz, R Kohen, R Mesika, Z Yakhini… - Methods, 2017 - Elsevier
RNA binding proteins (RBPs) play an important role in regulating many processes in the
cell. RBPs often recognize their RNA targets in a specific manner. In addition to the RNA …