A systematic search for RNA structural switches across the human transcriptome

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

doi:10.1038/s41592-024-02335-1

A systematic search for RNA structural switches across the human transcriptome

Nat Methods. 2024 Sep;21(9):1634-1645. doi: 10.1038/s41592-024-02335-1. Epub 2024 Jul 16.

Authors

Matvei Khoroshkin^{1

2

3

4}, Daniel Asarnow^{1

5}, Shaopu Zhou^{1

2

3

4}, Albertas Navickas^{1

2

3

4

6}, Aidan Winters^{2

3

4

7

8

9}, Jackson Goudreau^{1

2

3

4}, Simon K Zhou^{10

11}, Johnny Yu^{1

2

3

4}, Christina Palka¹², Lisa Fish^{1

2

3

4}, Ashir Borah^{1

2

3

4}, Kian Yousefi^{1

2

3

4}, Christopher Carpenter^{1

2

3

4}, K Mark Ansel^{10

11}, Yifan Cheng^{1

13}, Luke A Gilbert^{2

3

8

9}, Hani Goodarzi^{14

15

16

17

18}

Affiliations

¹ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
² Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
³ Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
⁴ Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
⁵ Department of Biochemistry, University of Washington, Seattle, WA, USA.
⁶ Institut Curie, UMR3348 CNRS, U1278 Inserm, Orsay, France.
⁷ Department of Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA.
⁸ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
⁹ Arc Institute, Palo Alto, CA, USA.
¹⁰ Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA.
¹¹ Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
¹² Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
¹³ Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
¹⁴ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. hani.goodarzi@ucsf.edu.
¹⁵ Department of Urology, University of California, San Francisco, San Francisco, CA, USA. hani.goodarzi@ucsf.edu.
¹⁶ Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA. hani.goodarzi@ucsf.edu.
¹⁷ Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA. hani.goodarzi@ucsf.edu.
¹⁸ Arc Institute, Palo Alto, CA, USA. hani.goodarzi@ucsf.edu.

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.

MeSH terms

3' Untranslated Regions
Computational Biology / methods
Cryoelectron Microscopy
Humans
Nonsense Mediated mRNA Decay
Nucleic Acid Conformation*
RNA / chemistry
RNA / genetics
Sulfuric Acid Esters / chemistry
Transcriptome*

Substances

3' Untranslated Regions
RNA
Sulfuric Acid Esters
dimethyl sulfate

Abstract

MeSH terms

Substances

Grants and funding