Pseudouridine Synthases Modify Human Pre-mRNA Co-transcriptionally and Affect Pre-mRNA Processing

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2022 Jan 20

PMID 35051350

Authors

Nicole M Martinez

Amanda Su

Margaret C Burns

Julia K Nussbacher

Cassandra Schaening

Shashank Sathe

Gene W Yeo

Wendy V Gilbert

Affiliations

Soon will be listed here.

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.

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