A Systematic Search for RNA Structural Switches Across the Human Transcriptome

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2024 Jul 16

PMID 39014073

Authors

Matvei Khoroshkin

Daniel Asarnow

Shaopu Zhou

Albertas Navickas

Aidan Winters

Jackson Goudreau

Simon K Zhou

Johnny Yu

Christina Palka

Lisa Fish

Ashir Borah

Kian Yousefi

Christopher Carpenter

K Mark Ansel

Yifan Cheng

Luke A Gilbert

Hani Goodarzi

Affiliations

Soon will be listed here.

Abstract

RNA structural switches are key regulators of gene expression in bacteria, but their characterization in Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3' untranslated region of the RORC (RAR-related orphan receptor C) transcript. In vivo dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated messenger RNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.

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