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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

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Updated: Jun 12, 2026

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

A nanopore-based HIV-1 reference epitranscriptome.

Michael S Bosmeny¹, Adrian A Pater¹, Li Zhang²

¹Department of Biochemistry, Wake Forest University, School of Medicine, Winston-Salem, NC 27101, United States.

Nucleic Acids Research

|March 19, 2026

Summary

This summary is machine-generated.

Researchers mapped RNA modifications in HIV-1, creating a reference epitranscriptome. This benchmark advances HIV-1 epitranscriptomics and provides a roadmap for studying other pathogens.

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Last Updated: Jun 12, 2026

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

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Published on: June 3, 2019

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV

Published on: March 5, 2022

Area of Science:

Molecular Biology
Virology
Genomics

Background:

Post-transcriptional modifications, forming the epitranscriptome, are crucial for RNA metabolism and gene regulation.
Challenges in mapping and functional characterization hinder epitranscriptomic studies.
Establishing reference epitranscriptomes is vital for data benchmarking and advancing the field.

Purpose of the Study:

To establish a reference epitranscriptome for human immunodeficiency virus 1 (HIV-1).
To map multiple RNA modifications at nucleotide resolution using advanced sequencing technology.
To provide a benchmark for HIV-1 epitranscriptomic research and a model for other pathogens.

Main Methods:

Sequencing of a model HIV-1 genome from infected T cells using nanopore technology.
Multiplexed base calling to map N6-methyladenosine (m6A), 5-methylcytidine, pseudouridine, inosine, and 2'-O-methyl modifications.
Correction of modification miscalling using synthetic RNA fragments and validation with an inhibitor.

Main Results:

A sense and preliminary antisense HIV-1 epitranscriptome were generated.
Modification patterns were consistent across different conditions, including combination antiretroviral therapy and in HIV-1 virions.
Substantial conservation of m6A modifications was observed in circulating HIV-1 strains from infected individuals.
Spliced transcript-dependent modification levels were identified.

Conclusions:

The study provides the first reference epitranscriptome for HIV-1, establishing a crucial benchmark.
The developed approach offers a roadmap for creating reference epitranscriptomes for other viruses and pathogens.
Findings advance the understanding of HIV-1 RNA modifications and their conservation in clinical strains.