Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap
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There is an increasing interest within the scientific community in identifying tRNA-derived fragments (tRFs) and elucidating the roles they play in the cell. Such endeavors can be greatly facilitated by mining the numerous datasets from many cellular contexts that exist publicly. However, the standard mapping tools cannot be used for the purpose. Several factors complicate this endeavor including: the presence of multiple identical or nearly identical isodecoders at various genomic locations; the presence of identical sequence segments that are shared by isodecoders of the same or even different anticodons; the existence of numerous partial tRNA sequences across the genome; the existence of hundreds of “lookalike” sequences that resemble true tRNAs; and others. This is generating a need for specialized tools that can mine deep sequencing data to identify and quantify tRFs. We discuss the various complicating factors and their ramifications, and how to use and run MINTmap, a tool that addresses these considerations.
Key wordsTransfer RNA tRNA tRNA-derived fragments tRFs tRF license plate internal tRFs i-tRFs 5′-halves 3′-halves 5′-tRFs tRNA-lookalikes MINTmap MINTsubmit MINTbase MINTcodes
The project was supported in part by a William Keck Foundation grant (IR), by Institutional Funds, and by a Commonwealth of Pennsylvania grant SAP#4100062221 (IR).
- 2.Huang HY, Hopper AK (2016) Multiple layers of stress-induced regulation in tRNA biology. Life 6(2). doi: 10.3390/life6020016
- 3.Orioli A (2017) tRNA biology in the omics era: stress signalling dynamics and cancer progression. Bioessays 39(3). doi: 10.1002/bies.201600158
- 7.Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, Rigoutsos I (2015) Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 6(28):24797–24822. doi: 10.18632/oncotarget.4695 CrossRefPubMedPubMedCentralGoogle Scholar
- 35.Rigoutsos I (2016) Comment on PMID 26673694:GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. In: PubMed Commons [Internet]. National Library of Medicine, Bethesda, MD. http://www.ncbi.nlm.nih.gov/pubmed/26673694-cm26673694_13813