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

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...

Full description

Saved in:
Bibliographic Details
Published in:Molecular cell 2022-02, Vol.82 (3), p.645-659.e9
Main Authors: Martinez, Nicole M., Su, Amanda, Burns, Margaret C., Nussbacher, Julia K., Schaening, Cassandra, Sathe, Shashank, Yeo, Gene W., Gilbert, Wendy V.
Format: Article
Language:English
Subjects:
alternative cleavage and polyadenylation
Alternative Splicing
Carcinoma, Hepatocellular - enzymology
Carcinoma, Hepatocellular - genetics
cotranscriptional
epitranscriptome
Gene Expression Regulation, Neoplastic
HEK293 Cells
Hep G2 Cells
Humans
Intramolecular Transferases - genetics
Intramolecular Transferases - metabolism
Liver Neoplasms - enzymology
Liver Neoplasms - genetics
mRNA modification
pre-mRNA processing
pseudouridine
pseudouridine synthase
RNA 3' End Processing
RNA modification
RNA Precursors - genetics
RNA Precursors - metabolism
RNA, Messenger - genetics
RNA, Messenger - metabolism
Transcription, Genetic
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. [Display omitted] •Pseudouridine RNA modifications are installed cotranscriptionally•Pre-mRNA pseudouridines are enriched in alternatively spliced regions•A single pseudouridine is sufficient to affect splicing efficiency in vitro•Three human pseudouridine synthases mediate widespread alternative pre-mRNA processing By profiling pseudouridines in chromatin-associated RNA, Martinez et al. demonstrate that pseudouridylation takes place cotranscriptionally in pre-mRNA. Multiple pseudouridine synthases directly modify pre-mRNA sequences in high-throughput biochemical assays. The depletion of pre-mRNA-modifying PUS, in turn, reveals a role for PUS in widespread pre-mRNA processing, including alternative splicing and 3′ end processing.
ISSN:1097-2765
1097-4164
DOI:10.1016/j.molcel.2021.12.023