Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number
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-gene...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | en_US |
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Oxford University Press
2014
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| Online Access: | http://hdl.handle.net/1721.1/92530 https://orcid.org/0000-0003-0011-3067 |
| _version_ | 1811093139797049344 |
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| author | Pang, Yan Ling Joy Abo, Ryan Levine, Stuart S. Dedon, Peter C |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Pang, Yan Ling Joy Abo, Ryan Levine, Stuart S. Dedon, Peter C |
| author_sort | Pang, Yan Ling Joy |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T15:40:20Z |
| format | Article |
| id | mit-1721.1/92530 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:40:20Z |
| publishDate | 2014 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/925302022-09-29T15:22:57Z Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number Pang, Yan Ling Joy Abo, Ryan Levine, Stuart S. Dedon, Peter C Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Biology Pang, Yan Ling Joy Abo, Ryan Levine, Stuart S. Dedon, Peter C. 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. National Institutes of Health (U.S.) (ES017010) National Institutes of Health (U.S.) (ES002109) National Science Foundation (U.S.) (CHE-1308839) Singapore-MIT Alliance for Research and Technology 2014-12-29T18:55:38Z 2014-12-29T18:55:38Z 2014-10 2014-09 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/92530 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. https://orcid.org/0000-0003-0011-3067 en_US http://dx.doi.org/10.1093/nar/gku945 Nucleic Acids Research Creative Commons Attribution http://creativecommons.org/licenses/by-nc/4.0 application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Pang, Yan Ling Joy Abo, Ryan Levine, Stuart S. Dedon, Peter C Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number |
| title | Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number |
| title_full | Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number |
| title_fullStr | Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number |
| title_full_unstemmed | Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number |
| title_short | Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number |
| title_sort | diverse cell stresses induce unique patterns of trna up and down regulation trna seq for quantifying changes in trna copy number |
| url | http://hdl.handle.net/1721.1/92530 https://orcid.org/0000-0003-0011-3067 |
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