Protocol for mapping RNA G-quadruplex for chromatin-bound RNA using d-rG4-seq

Abstract

Summary: Here, we present a protocol for using d-rG4-seq, a technique for mapping RNA G-quadruplex (rG4) for chromatin-bound RNA. We describe steps for identifying in vivo rG4 structures based on differential sensitivity of rG4 to dimethyl sulfate (DMS) modification, folding in the presence of monovalent cations, K+ versus Li+, and reverse transcriptase (RT) readthrough when folded. We then detail procedures for isolating RNA from the chromatin-bound fractions to enrich for epigenetic regulators and comparing in vitro versus in vivo profiles.For complete details on the use and execution of this protocol, please refer to Lee et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Genomics
• Molecular Biology
• Gene Expression