Cited by 52RNA modifications and cancerRNA regulation and diseaseRNA and protein synthesis mechanisms

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

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Baek, Alice, Lee, Ga-Eun, Golconda, Sarah, Rayhan, Asif, Manganaris, Anastasios A., Chen, Shuliang, Tirumuru, Nagaraja, Yu, Hannah +7 more·2024·Nature Microbiology

Published version of a preprint

Abstract

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

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  • Demethylated RNA is more efficiently packaged, while the methylated form (m6A-marked RNA) supports translation.

    “demethylated RNA is more efficiently packaged, while the methylated form (m6A-marked RNA) supports translation”

    From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Baek et al. 2024

    The Results (‘Higher m6A stoichiometry on HIV-1 mRNAs than genomic RNA’; ‘Triple m6A mutations reduced HIV-1 protein translation’) report more m6A on translating HIV-1 mRNAs and reduced translation after mutation of three m6A sites. But the packaging claim is stronger than the paper’s finding: the Results say fewer m6As on genomic RNA *may* be favoured during packaging, and the Discussion says the mechanism needs further investigation. The paper does not establish that demethylated RNA is packaged more efficiently. (LLM, conf=0.87)

    Experimental — accuracy not yet measured
  • RNA modifications, particularly N6-methyladenosine (m6A), impact gRNA fate.

    “RNA modifications, particularly N6-methyladenosine (m6A), impact gRNA fate.”

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Authors
Baek, A., Lee, G.-E., Golconda, S., Rayhan, A., Manganaris, A. A., Chen, S., Tirumuru, N., Yu, H., Kim, S., Kimmel, C., Zablocki, O., Sullivan, M. B., Addepalli, B., Wu, L., & Kim, S.
Affiliations
  • The Ohio State University (US)
  • University of Cincinnati (US)
  • University of Iowa (US)
Corresponding author
  • Kim, Shihyoung
  • Kim, Sanggu
Venue
Nature Microbiology
Published
2024-04-11
Volume
9
Issue
5
Pages
1340-1355
ISSN
2058-5276 (ISSN-L)
OpenAlex
W4394718034
Cited by
52
References
112
Citations by year
2026: 13 · 2025: 26 · 2024: 13
FWCI
7.08
Type
journal article
Language
en
Open access
Locations
  • Nature Microbiology (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders
  • U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (R01HG010318, HG010108)
  • U.S. Department of Defense (HT9425-23-1-0582)
  • University of Cincinnati
  • U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (R61AI169659, R21AI170070)
  • U.S. Department of Energy (248445, DE-SC0023307)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
HIV-1, N6-methyladenosine, epitranscriptomics, RNA modification, single-molecule RNA sequencing, viral RNA splicing, viral RNA translation, RNA stability, 3'-end modification, HIV-1 replication
MeSH terms
Adenosine, Humans, RNA Splicing, RNA, Messenger, RNA, Viral, Virus Replication, HIV-1, HIV Infections, Sequence Analysis, RNA, Transcriptome

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