{"title":"Bioinformatics of simultaneous, quantitative measurements of full-length tRNA and tRNA fragments by MSR sequencing.","authors":"Luke R Frietze, Tao Pan","doi":"10.1016/bs.mie.2024.11.009","DOIUrl":null,"url":null,"abstract":"<p><p>tRNA fragments (tRFs) are generated by cellular endogenous ribonuclease cleavage and play important roles in cellular processes and diseases states. Many questions regarding tRF functions remain to be studied and understood. Common sequencing techniques measure tRF after a size selection step that separates the full-length tRNA and tRF before sequencing library construction. The crucial information on the relationship of tRFs to their respective full-length tRNA in the same biological sample cannot be obtained in this way. We developed multiplex small RNA sequencing (MSR-seq) which measures the abundance as well as site-specific modification information on both full-length tRNA and their matching tRFs in the same sample. Here we describe the bioinformatic steps to obtain the tRF abundance data from the MSR-seq data using the publicly available pipeline in Github (https://github.com/Luke-F1875/MSRseq_data_processing_pipeline).</p>","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"711 ","pages":"312-323"},"PeriodicalIF":0.0000,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Methods in enzymology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/bs.mie.2024.11.009","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/11/22 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
Bioinformatics of simultaneous, quantitative measurements of full-length tRNA and tRNA fragments by MSR sequencing.
tRNA fragments (tRFs) are generated by cellular endogenous ribonuclease cleavage and play important roles in cellular processes and diseases states. Many questions regarding tRF functions remain to be studied and understood. Common sequencing techniques measure tRF after a size selection step that separates the full-length tRNA and tRF before sequencing library construction. The crucial information on the relationship of tRFs to their respective full-length tRNA in the same biological sample cannot be obtained in this way. We developed multiplex small RNA sequencing (MSR-seq) which measures the abundance as well as site-specific modification information on both full-length tRNA and their matching tRFs in the same sample. Here we describe the bioinformatic steps to obtain the tRF abundance data from the MSR-seq data using the publicly available pipeline in Github (https://github.com/Luke-F1875/MSRseq_data_processing_pipeline).
期刊介绍：
The critically acclaimed laboratory standard for almost 50 years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 500 volumes the series contains much material still relevant today and is truly an essential publication for researchers in all fields of life sciences, including microbiology, biochemistry, cancer research and genetics-just to name a few. Five of the 2013 Nobel Laureates have edited or contributed to volumes of MIE.
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