{"title":"Resolving sequencing-based HIV-1 epitranscriptomics.","authors":"Michael S Bosmeny, Joao I Mamede, Keith T Gagnon","doi":"10.1080/17501911.2025.2504333","DOIUrl":null,"url":null,"abstract":"<p><p>The collection of HIV-1 RNA chemical modifications and their functional consequences in viral gene expression, host interactions, and the viral life cycle, referred to as HIV-1 epitranscriptomics, remain incompletely understood. While the field is evolving, diverse modification discovery methods, cell lines, HIV-1 sequences, and bioinformatics methods make a consensus view of the HIV-1 epitranscriptome difficult to resolve. Here, we review methods for identifying and interpreting N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), 5-methylcytosine (m<sup>5</sup>C), pseudouridine (Ψ), 2´-<i>O</i>-methylation (N<sub>m</sub>), and N<sup>4</sup>-acetylcytidine (ac<sup>4</sup>C) modifications in HIV-1, including antibody-based selection methods, chemical-treatment-based selection methods, and detection by nanopore direct RNA sequencing. We recommend the adoption of the latter as a standardized sequencing strategy to enable better benchmarking across diverse studies and help resolve HIV-1 epitranscriptomics.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-12"},"PeriodicalIF":3.0000,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Epigenomics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1080/17501911.2025.2504333","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
Abstract
The collection of HIV-1 RNA chemical modifications and their functional consequences in viral gene expression, host interactions, and the viral life cycle, referred to as HIV-1 epitranscriptomics, remain incompletely understood. While the field is evolving, diverse modification discovery methods, cell lines, HIV-1 sequences, and bioinformatics methods make a consensus view of the HIV-1 epitranscriptome difficult to resolve. Here, we review methods for identifying and interpreting N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine (Ψ), 2´-O-methylation (Nm), and N4-acetylcytidine (ac4C) modifications in HIV-1, including antibody-based selection methods, chemical-treatment-based selection methods, and detection by nanopore direct RNA sequencing. We recommend the adoption of the latter as a standardized sequencing strategy to enable better benchmarking across diverse studies and help resolve HIV-1 epitranscriptomics.
期刊介绍:
Epigenomics provides the forum to address the rapidly progressing research developments in this ever-expanding field; to report on the major challenges ahead and critical advances that are propelling the science forward. The journal delivers this information in concise, at-a-glance article formats – invaluable to a time constrained community.
Substantial developments in our current knowledge and understanding of genomics and epigenetics are constantly being made, yet this field is still in its infancy. Epigenomics provides a critical overview of the latest and most significant advances as they unfold and explores their potential application in the clinical setting.