Researchers Develop Sequencing Method to Detect RNA Modifications on Viral RNAs

Matthew Weitzman, PhD Researchers at Children’s Hospital of Philadelphia (CHOP) and the Perelman School of Medicine at the University of Pennsylvania, in collaboration with scientists at the New York University School of Medicine, have developed a sequencing method to detect RNA modifications that regulate RNA splicing during adenovirus infection. The resulting study, which also involved input from other institutions, including Duke University and Weill Cornell Medicine, was recently published in Nature Communications.

Adenovirus is a DNA virus that uses the host’s cell machinery to replicate and infect the host. Processing and metabolism of cellular RNAs can be regulated by METTL3, a protein coding gene that catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. Previous studies have shown that m6A is implicated in regulating multiple processes of RNA maturation, including splicing, translation, and ultimately decay. However, until recently, sequencing techniques to map m6A on viral RNA have been indirect and labor intensive, and so the location and function of this mark within the infectious cycle was unknown.

To map m6A more accurately within the adenovirus transcriptome, the researchers used a combination of short- and long-read RNA sequencing to pinpoint m6A at the nucleotide and transcript level. The researchers found that although both early and late viral transcripts contain m6A, depletion of METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. Given that nuclear RNA decay pathways target unspliced cellular RNAs for destruction, the researchers hypothesize that by facilitating efficient splicing, m6A leads to the accumulation of mature viral mRNAs that would otherwise be destroyed in the nucleus before being translated in the cytoplasm.

“These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution,” said Matthew Weitzman, PhD, a Professor in the Department of Pathology and Laboratory Medicine at CHOP and senior author of the paper. “This work also highlights how RNA modifications can regulate distinct stages of viral gene expression.”

Read more about this research here.