解决基于测序的HIV-1表转录组学。

IF 3 4区 医学 Q2 GENETICS & HEREDITY
Michael S Bosmeny, Joao I Mamede, Keith T Gagnon
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引用次数: 0

摘要

HIV-1 RNA化学修饰的收集及其在病毒基因表达、宿主相互作用和病毒生命周期中的功能后果,被称为HIV-1表转录组学,仍未完全了解。随着该领域的不断发展,各种修饰发现方法、细胞系、HIV-1序列和生物信息学方法使得HIV-1表转录组的共识观点难以解决。在这里,我们回顾了鉴定和解释HIV-1中n6 -甲基腺苷(m6A)、5-甲基胞嘧啶(m5C)、假尿嘧啶(Ψ)、2´- o -甲基化(Nm)和n4 -乙酰胞苷(ac4C)修饰的方法,包括基于抗体的选择方法、基于化学处理的选择方法和纳米孔直接RNA测序检测。我们建议采用后者作为标准化的测序策略,以便在不同的研究中更好地进行基准测试,并帮助解决HIV-1表转录组学问题。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Resolving sequencing-based HIV-1 epitranscriptomics.

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.

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来源期刊
Epigenomics
Epigenomics GENETICS & HEREDITY-
CiteScore
5.80
自引率
2.60%
发文量
95
审稿时长
>12 weeks
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.
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