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mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation
Caroline A McCormick1, Michele Meseonznik1, Yuchen Qiu1
1Dept. of Bioengineering, Northeastern University, Boston, MA.
Biorxiv : the Preprint Server for Biology
|May 20, 2024
Summary
Pseudouridine (psi) modifications in human mRNA are mapped transcriptome-wide using Nanopore sequencing. Cell type influences psi levels, impacting gene expression and protein production.
Area of Science:
- * Molecular Biology
- * Genomics
- * RNA Biology
Background:
- * Pseudouridine (psi) is a prevalent mRNA modification synthesized by enzymes like TRUB1 and PUS7.
- * Understanding psi's role requires accurate transcriptome-wide mapping and analysis of its positional occupancy.
Purpose of the Study:
- * To map positional pseudouridine occupancy across diverse human cell types.
- * To investigate the impact of psi on gene expression and translation.
- * To identify cell type-specific pseudouridylation patterns.
Main Methods:
- * Utilized Nanopore direct RNA sequencing for transcriptome-wide psi mapping.
- * Employed the Mod-p ID tool for accurate identification of pseudouridine sites without chemical modification or cDNA conversion.
- * Compared positional psi occupancy across six immortalized human cell lines from various tissue types.
Main Results:
- * Lung-derived cells exhibited the highest proportion of pseudouridine, while liver-derived cells showed the lowest.
- * Conserved pseudouridine sites on mRNAs correlated with increased protein production, suggesting a role in translation regulation.
- * Identified cell type-specific pseudouridine modifications in ubiquitously expressed genes.
- * Characterized transcripts with multiple conserved or cell type-specific pseudouridine modifications, including within the same motif.
Conclusions:
- * Pseudouridine modifications play a significant role in regulating translation.
- * Cell type-specific trans-acting factors are crucial drivers of pseudouridylation patterns.
- * Nanopore direct RNA sequencing with Mod-p ID offers a sensitive method for studying positional psi occupancy and its functional implications.
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