Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion

Jonathan C Schmok; Manya Jain; Lena A Street; Alex T Tankka; Danielle Schafer; Hsuan-Lin Her; Sara Elmsaouri; Maya L Gosztyla; Evan A Boyle; Pratibha Jagannatha; En-Ching Luo; Ester J Kwon; Marko Jovanovic; Gene W Yeo

doi:10.1038/s41587-023-02014-0

Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion

Nat Biotechnol. 2024 Jan 2. doi: 10.1038/s41587-023-02014-0. Online ahead of print.

Authors

Jonathan C Schmok^{1

2

3

4}, Manya Jain^{1

2

3}, Lena A Street⁵, Alex T Tankka^{1

2

3}, Danielle Schafer^{1

2

3}, Hsuan-Lin Her^{1

2

3}, Sara Elmsaouri^{1

2

3}, Maya L Gosztyla^{1

2

3}, Evan A Boyle^{1

2

3}, Pratibha Jagannatha^{1

2

3}, En-Ching Luo^{1

2

3}, Ester J Kwon⁴, Marko Jovanovic⁵, Gene W Yeo^{6

7

8}

Affiliations

¹ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
² Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
³ Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
⁴ Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
⁵ Department of Biological Sciences, Columbia University, New York, NY, USA.
⁶ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. geneyeo@ucsd.edu.
⁷ Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA. geneyeo@ucsd.edu.
⁸ Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA. geneyeo@ucsd.edu.

PMID: 38168984
DOI: 10.1038/s41587-023-02014-0

Abstract

RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification-mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.

Abstract

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