An HIV-1 Reference Epitranscriptome DOI Creative Commons

Michael S. Bosmeny,

Adrian A. Pater,

Li Zhang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

ABSTRACT Post-transcriptional chemical modifications to RNA, or the epitranscriptome, play important roles in RNA metabolism, gene regulation, and human disease, including viral pathogenesis. Modifications genome transcripts of immunodeficiency virus 1 (HIV-1) have been reported, methylation adenosine (m 6 A) cytosine 5 C), acetylation cytosine, pseudouridylation (psi), conversion inosine, their effects on host biology investigated. However, diverse experimental approaches used, making clear correlations across studies difficult assess. To address this need, we propose establishment a reference HIV-1 epitranscriptome. We sequenced model NL4-3 from infected Jurkat CD4+ T cells using latest nanopore chemistry, custom preparation methods, commercial base-calling algorithms. This resulted reproducible sense preliminary antisense epitranscriptome where m A, C, psi, ands inosine could be identified by multiplexed base-calling. Multiplexed miscalled due sequence neighboring modification contexts, which demonstrate can corrected with synthetic fragments. validate A sites small molecule inhibitor methyltransferase-like 3 (METTL3), STM2457. conclude that do not change substantially under combination antiretroviral therapy (cART) treatment primary cells. Samples patients living HIV reveal conservation certain modifications, such as A. Our approach data offer straightforward benchmark adopted help advance rigor, reproducibility, uniformity future epitranscriptomics studies.

Language: Английский

An HIV-1 Reference Epitranscriptome DOI Creative Commons

Michael S. Bosmeny,

Adrian A. Pater,

Li Zhang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

ABSTRACT Post-transcriptional chemical modifications to RNA, or the epitranscriptome, play important roles in RNA metabolism, gene regulation, and human disease, including viral pathogenesis. Modifications genome transcripts of immunodeficiency virus 1 (HIV-1) have been reported, methylation adenosine (m 6 A) cytosine 5 C), acetylation cytosine, pseudouridylation (psi), conversion inosine, their effects on host biology investigated. However, diverse experimental approaches used, making clear correlations across studies difficult assess. To address this need, we propose establishment a reference HIV-1 epitranscriptome. We sequenced model NL4-3 from infected Jurkat CD4+ T cells using latest nanopore chemistry, custom preparation methods, commercial base-calling algorithms. This resulted reproducible sense preliminary antisense epitranscriptome where m A, C, psi, ands inosine could be identified by multiplexed base-calling. Multiplexed miscalled due sequence neighboring modification contexts, which demonstrate can corrected with synthetic fragments. validate A sites small molecule inhibitor methyltransferase-like 3 (METTL3), STM2457. conclude that do not change substantially under combination antiretroviral therapy (cART) treatment primary cells. Samples patients living HIV reveal conservation certain modifications, such as A. Our approach data offer straightforward benchmark adopted help advance rigor, reproducibility, uniformity future epitranscriptomics studies.

Language: Английский

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