Decoding murine cytomegalovirus.

Area of Science:

• Virology
• Genomics
• Molecular Biology

Background:

• The genomes of human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) were sequenced decades ago, initially thought to have ~170 open reading frames (ORFs).
• Recent omics studies show HCMV gene expression is far more complex, with hundreds of viral ORFs.

Purpose of the Study:

• To provide a state-of-the-art reannotation of lytic MCMV gene expression using integrative omics data.
• To characterize the complexity and kinetics of MCMV transcription and identify novel viral genes and regulatory elements.

Main Methods:

• Integrative analysis of a large omics dataset.
• Transcription start site (TiSS) profiling.
• Metabolic RNA labeling and sequencing (dSLAM-seq).

Main Results:

• Identification of 365 viral TiSS, leading to 380 transcripts and 454 ORFs, including over 200 small ORFs.
• Discovery of a novel immediate-early transcript (ie4) and late-induced transcripts with initiator elements but no TATA-box.
• Demonstration that viral upstream ORFs (uORFs) regulate translation of downstream ORFs.
• Identification of a truncated m145 isoform that doesn't affect NK cell ligand downregulation.

Conclusions:

• This comprehensive reannotation significantly expands the known MCMV transcriptome.
• The findings reveal novel viral gene products and regulatory strategies, including uORF-mediated translational control.
• This work provides a foundation for future studies on uncharacterized MCMV genes in a key animal model.