Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST
Overview
Affiliations
RNA transcripts can form a variety of higher-order structures. We developed a large-scale affinity analysis system, FOREST (Folded RNA Element Profiling with Structure Library), to investigate the function of these RNA structures on transcriptome-wide scale. Here we describe a protocol to analyze RNA-protein interactions using FOREST . Users of the protocol prepare an RNA structure library comprised of diverse species of transcripts and perform high-throughput characterization of the RNA-protein interactions to obtain quantitative and comprehensive information on the binding affinities and specificities. Moreover, we demonstrate how FOREST can be used to analyze a non-canonical structure, the RNA G-quadruplex, without sequencing bias, because the quantification is performed directly on a microarray without sequence amplification. FOREST will contribute to the discovery of RNA structure motifs that determine RNA-protein interactions.
A Blue Light-Responsive Strong Synthetic Promoter Based on Rational Design in .
Chen C, Chen J, Wu G, Li L, Hu Z, Li X Int J Mol Sci. 2023; 24(19).
PMID: 37834043 PMC: 10572394. DOI: 10.3390/ijms241914596.
Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K Plant Commun. 2023; 4(4):100558.
PMID: 36760129 PMC: 10363483. DOI: 10.1016/j.xplc.2023.100558.