Genomics

Dataset Information

0

Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique


ABSTRACT: Pseudouridine (ψ) is the most common non-canonical ribonucleoside present on mammalian non-coding RNAs (ncRNAs), where is contributes ~10% of the total uridine level. However, ψ constitutes only ~0.3% of the uridines present on mRNAs and its effect on mRNA function remains unclear. Ψ residues have however been shown to inhibit the detection of exogenous RNA transcripts by host innate immune factors, thus raising the possibility that viruses might have subverted the addition of ψ residues to mRNAs by host pseudouridine synthase (PUS) enzymes as a way to inhibit antiviral responses in infected cells. Here, we describe and validate a novel antibody-based ψ mapping technique called photo-crosslinking assisted ψ sequencing (PA-ψ-seq) and then use it to map ψ residues on not only multiple cellular RNAs but also the mRNAs and genomic RNA encoded by HIV-1. We also describe several 293T-derived cell lines in which human PUS enzymes previously reported to add ψ residues to mRNAs, specifically PUS1, PUS7 and TRUB1/PUS4, were individually inactivated by gene editing. Surprisingly, while this allowed us to assign several sites of ψ addition on cellular mRNAs to each of these three PUS enzymes, the ψ sites present on HIV-1 transcripts remained unaffected. However, loss of PUS1 function did significantly reduce HIV-1 gene expression by a presumably indirect mechanism.

ORGANISM(S): Homo sapiens

PROVIDER: GSE172136 | GEO | 2021/09/01

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2024-02-26 | GSE229980 | GEO
2022-02-15 | GSE123613 | GEO
2024-07-31 | GSE241849 | GEO
2023-02-06 | GSE212210 | GEO
2019-11-21 | GSE124558 | GEO
2015-06-05 | E-GEOD-63655 | biostudies-arrayexpress
2016-05-16 | E-GEOD-77819 | biostudies-arrayexpress
2016-05-16 | E-GEOD-77821 | biostudies-arrayexpress
2016-05-16 | E-GEOD-77820 | biostudies-arrayexpress
2016-05-16 | E-GEOD-77822 | biostudies-arrayexpress