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

Area of Science:

• Epitranscriptomics
• Molecular Biology
• Virology

Background:

• RNA modifications like N6-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C) are crucial regulatory layers in cellular processes.
• Epitranscriptomics, the study of these modifications, is vital for understanding gene regulation beyond transcriptomics.
• Viral infections can alter cellular epitranscriptomic landscapes.

Purpose of the Study:

• To develop and present a workflow for simultaneous analysis of m⁶A and m⁵C RNA modifications.
• To investigate the joint epitranscriptomic landscape in cells infected with human immunodeficiency virus (HIV).
• To identify differentially methylated transcripts in response to viral infection.

Main Methods:

• Utilized MeRIP-Seq to enrich for m⁶A-modified RNA fragments.
• Employed BS-Seq for single-nucleotide resolution identification of m⁵C marks.
• Developed a bioinformatics pipeline to analyze methylation data independently of expression levels.

Main Results:

• Successfully established a method for simultaneous epitranscriptomic analysis of m⁶A and m⁵C.
• Generated an atlas of differentially methylated transcripts in HIV-infected cells.
• Demonstrated the capability to identify changes in RNA modifications upon viral infection.

Conclusions:

• The presented methodology enables simultaneous exploration of multiple epitranscriptomic marks.
• This approach provides new opportunities to discover novel cellular factors and mechanisms involved in antiviral responses.
• The workflow is applicable to studying epitranscriptomic alterations in various cell perturbations, including viral infections.