2. Academic Validation
  3. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing

  • Mol Cell. 2022 Feb 3;82(3):645-659.e9. doi: 10.1016/j.molcel.2021.12.023.
Nicole M Martinez 1,  Amanda Su 1,  Margaret C Burns 2,  Julia K Nussbacher 2,  Cassandra Schaening 3,  Shashank Sathe 2,  Gene W Yeo 4,  Wendy V Gilbert 5
Affiliations

Affiliations

  • 1 Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA.
  • 2 Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
  • 3 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
  • 4 Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: geneyeo@ucsd.edu.
  • 5 Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA. Electronic address: wendy.gilbert@yale.edu.
PMID: 35051350 DOI: 10.1016/j.molcel.2021.12.023
Abstract

Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine profiling on chromatin-associated RNA from human cells, we identified pseudouridines in nascent pre-mRNA at locations associated with alternatively spliced regions, enriched near splice sites, and overlapping hundreds of binding sites for RNA-binding proteins. In vitro splicing assays establish a direct effect of individual endogenous pre-mRNA pseudouridines on splicing efficiency. We validate hundreds of pre-mRNA sites as direct targets of distinct pseudouridine synthases and show that PUS1, PUS7, and RPUSD4-three pre-mRNA-modifying pseudouridine synthases with tissue-specific expression-control widespread changes in alternative pre-mRNA splicing and 3' end processing. Our results establish a vast potential for cotranscriptional pre-mRNA pseudouridylation to regulate human gene expression via alternative pre-mRNA processing.

Keywords

RNA modification; alternative cleavage and polyadenylation; alternative splicing; cotranscriptional; epitranscriptome; mRNA modification; pre-mRNA processing; pseudouridine; pseudouridine synthase.

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