Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs.

Diverse conditions of infection and cellular stress incite the cleavage of transfer RNAs, leading to the formation of tRNA fragments which can directly regulate gene expression. In our study of gammaherpesviruses, such as the murine herpesvirus 68 and human oncogenic Kaposi Sarcoma associated Herpesvirus, we discovered that transfer RNA regulation and cleavage is a key component of gene reprogramming during infection. We present the first in-depth profile of tRNA fragment generation in response to DNA virus infection, using state-of-the-art sequencing techniques that overcome several challenges with tRNA sequencing. We present several lines of evidence that tRNA fragments are made from newly-transcribed premature tRNAs and propose that this may be a defining characteristic of tRNA cleavage in some contexts. Finally, we show that tRNA splicing machinery is involved with the formation of some MHV68-induced tRNA fragments, with a key regulator of splicing, CLP1, required for maximal viral titer. Together, we posit that tRNA processing may be integral to the elegant shift in gene expression that occurs during viral take-over of the host cell.