Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(5), P. 1340 - 1355

Published: April 11, 2024

Abstract Although the significance of chemical modifications on RNA is acknowledged, evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values for fragmented RNAs at low resolution relied indirect analyses phenotypic effects by perturbing host effectors. Here we analysed HIV-1 full-length, single level nucleotide using direct sequencing methods. Our data reveal an unexpectedly simple modification landscape, highlighting three predominant N 6 -methyladenosine (m A) near 3′ end. More densely installed spliced viral messenger than genomic RNAs, these m As play a crucial role maintaining normal levels splicing translation. generates diverse subspecies with distinct A ensembles, multiple its provides additional stability resilience to replication, suggesting unexplored RNA-level strategy.

Language: Английский

YTHDF1 and YTHDC1 m ⁶ A reader proteins regulate HTLV-1 tax and hbz activity

Journal of Virology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 4, 2025

ABSTRACT Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus responsible for adult leukemia/lymphoma (ATLL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), progressive neurodegenerative disease. Regulation of viral gene expression plays key role in persistence pathogenesis. However, the molecular mechanisms underlying this fine-tuned regulation remain poorly understood. Little known regarding RNA chemical modifications HTLV-1 how these affect biology disease development. Post-transcriptional modification common eukaryotes, with N 6 -methyladenosine (m A) being most prevalent. In study, we investigated m A on expression. Using MeRIP-Seq, mapped sites to 3’ end genome. We found RNA, as well oncogene transcripts tax hbz , contained modifications. A-depletion HTLV-1-transformed cells decreased sense-derived genes ( Tax, Gag, Env ) increased antisense-derived Hbz Tax were bound by reader proteins YTHDF1 YTHDC1 panel lines. vectors shRNA-mediated knockdown, that had opposing effects expression, decreasing increasing . Upon further abundance dependent deposition. The nuclear protein affected both sense- specifically enhanced export transcript. Collectively, our results demonstrate global levels regulate IMPORTANCE pathogenesis are controlled through tight fate can be epigenetic impact without altering DNA sequence. Our study details N6-methyladenosine reductions other genes, whereas suggest oncogenic transcripts, A-modified cells. interpreted YTHDC1, which dictate RNA. Understanding offers potential insights into novel therapeutic strategies diseases.

Language: Английский

Resolving sequencing-based HIV-1 epitranscriptomics

Epigenomics, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 12

Published: May 16, 2025

The collection of HIV-1 RNA chemical modifications and their functional consequences in viral gene expression, host interactions, the life cycle, referred to as epitranscriptomics, remain incompletely understood. While field is evolving, diverse modification discovery methods, cell lines, sequences, bioinformatics methods make a consensus view epitranscriptome difficult resolve. Here, we review for identifying interpreting N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine (Ψ), 2´-O-methylation (Nm), N4-acetylcytidine (ac4C) HIV-1, including antibody-based selection chemical-treatment-based detection by nanopore direct sequencing. We recommend adoption latter standardized sequencing strategy enable better benchmarking across studies help resolve epitranscriptomics.

Language: Английский