» Articles » PMID: 35796970

Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST

Overview
Specialty Molecular Biology
Date 2022 Jul 7
PMID 35796970
Authors
Affiliations
Soon will be listed here.
Abstract

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.

Citing Articles

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.


Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.

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.

References
1.
Yao Z, Weinberg Z, Ruzzo W . CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics. 2005; 22(4):445-52. DOI: 10.1093/bioinformatics/btk008. View

2.
Nawrocki E, Eddy S . Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013; 29(22):2933-5. PMC: 3810854. DOI: 10.1093/bioinformatics/btt509. View

3.
Siegfried N, Busan S, Rice G, Nelson J, Weeks K . RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods. 2014; 11(9):959-65. PMC: 4259394. DOI: 10.1038/nmeth.3029. View

4.
Lu Z, Zhang Q, Lee B, Flynn R, Smith M, Robinson J . RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016; 165(5):1267-1279. PMC: 5029792. DOI: 10.1016/j.cell.2016.04.028. View

5.
Mustoe A, Busan S, Rice G, Hajdin C, Peterson B, Ruda V . Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. Cell. 2018; 173(1):181-195.e18. PMC: 5866243. DOI: 10.1016/j.cell.2018.02.034. View