Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number
Author(s)Pang, Yan Ling Joy; Abo, Ryan; Levine, Stuart S.; Dedon, Peter C.
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Emerging evidence points to roles for tRNA modifications and tRNA abundance in cellular stress responses. While isolated instances of stress-induced tRNA degradation have been reported, we sought to assess the effects of stress on tRNA levels at a systems level. To this end, we developed a next-generation sequencing method that exploits the paucity of ribonucleoside modifications at the 3′-end of tRNAs to quantify changes in all cellular tRNA molecules. Application of this tRNA-seq method to Saccharomyces cerevisiae identified all 76 expressed unique tRNA species out of 295 coded in the yeast genome, including all isoacceptor variants, with highly precise relative (fold-change) quantification of tRNAs. In studies of stress-induced changes in tRNA levels, we found that oxidation (H[subscript 2]O[subscript 2]) and alkylation (methylmethane sulfonate, MMS) stresses induced nearly identical patterns of up- and down-regulation for 58 tRNAs. However, 18 tRNAs showed opposing changes for the stresses, which parallels our observation of signature reprogramming of tRNA modifications caused by H[subscript 2]O[subscript 2] and MMS. Further, stress-induced degradation was limited to only a small proportion of a few tRNA species. With tRNA-seq applicable to any organism, these results suggest that translational control of stress response involves a contribution from tRNA abundance.
DepartmentMassachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Department of Biology
Nucleic Acids Research
Oxford University Press
Pang, Yan Ling Joy, Ryan Abo, Stuart S. Levine, and Peter C. Dedon. “Diverse Cell Stresses Induce Unique Patterns of tRNA up- and down-Regulation: tRNA-Seq for Quantifying Changes in tRNA Copy Number.” Nucleic Acids Research 42, no. 22 (October 27, 2014): e170–e170.
Final published version