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Probing Transcriptome-Wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2.

Probing Transcriptome-Wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2.

Authors :
Lai YH
Tran EJ
Source :
Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2209, pp. 287-305.
Publication Year :
2021

Abstract

RNA helicases function in all aspects of RNA biology mainly through remodeling structures of RNA and RNA-protein (RNP) complexes. Among them, DEAD-box proteins form the largest family in eukaryotes and have been shown to remodel RNA/RNP structures and clamping of RNA-binding proteins, both in vitro and in vivo. Nevertheless, for the majority of these enzymes, it is largely unclear what RNAs are targeted and where they modulate RNA/RNP structures to promote RNA metabolism. Several methods have been developed to probe secondary and tertiary structures of specific transcripts or whole transcriptomes in vivo. In this chapter, we describe a protocol for identification of RNA structural changes that are dependent on a Saccharomyces cerevisiae DEAD-box helicase Dbp2. Experiments detailed here can be adapted to the study of other RNA helicases and identification of putative remodeling targets in vivo.

Details

Language :
English
ISSN :
1940-6029
Volume :
2209
Database :
MEDLINE
Journal :
Methods in molecular biology (Clifton, N.J.)
Publication Type :
Academic Journal
Accession number :
33201476
Full Text :
https://doi.org/10.1007/978-1-0716-0935-4_18