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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
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Characterizing transcripts of HIV-1 different substrains using direct RNA sequencing.
Weizhen Li1,2, Yong Huang2, Haowen Yuan3
1School of Public Health and Health Management, Gannan Medical University, Ganzhou, Jiangxi, 341000, China.
Heliyon
|November 8, 2024
Summary
This study analyzes HIV-1 RNA processing and modifications using direct RNA sequencing. It identifies novel splicing sites and chemical modifications in two HIV-1 subtypes, offering potential new therapeutic targets.
Area of Science:
- Virology
- Molecular Biology
- Genomics
Background:
- Post-transcriptional modifications of viral RNA are critical for gene expression, stability, and replication.
- Understanding these modifications in Human Immunodeficiency Virus type 1 (HIV-1) is key for developing antiviral therapies.
Purpose of the Study:
- To comprehensively analyze the transcriptome and epitranscriptome of HIV-1 subtype B (NL4-3) and CRF01_AE (GX2005002) strains.
- To identify novel splicing sites, chemically modified sites, and N6-methyladenosine (m6A) modifications in these HIV-1 strains.
Main Methods:
- Utilized Oxford Nanopore Technology (ONT) direct RNA sequencing (DRS).
- Analyzed RNA isoforms, splicing sites, poly(A) tail lengths, and chemical modifications.
Main Results:
- Identified 11 novel splicing sites in NL4-3 (out of 61 isoforms) and defined splicing sites for GX2005002 (63 isoforms).
- Detected 74 and 79 chemically modified sites in NL4-3 and GX2005002 transcripts, respectively.
- Found three conserved m6A modification sites in both strains, with no correlation between poly(A) tail length and modification sites.
Conclusions:
- Provides a detailed characterization of post-transcriptional RNA processing and modifications in two distinct HIV-1 subtypes.
- Highlights potential new therapeutic targets for HIV treatment based on identified RNA features.
Keywords:
Alternative splicingHIV-1 transcriptsNanopore direct RNA sequencingPolyadenylationRNA modificationMore Related Videos
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