Consequential considerations when mapping tRNA fragments

We examine several of the choices that went into the design of tDRmapper, a recently reported tool for identifying transfer RNA (tRNA) fragments in deep sequencing data, evaluate them in the context of currently available knowledge, and discuss their potential impact on the output that the tool generates.

[1]  Aristeidis G Telonis,et al.  Mitochondrial tRNA-lookalikes in nuclear chromosomes: Could they be functional? , 2015, RNA biology.

[2]  Praveen Sethupathy,et al.  tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data , 2015, BMC Bioinformatics.

[3]  Phillipe Loher,et al.  Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers , 2015, Proceedings of the National Academy of Sciences.

[4]  Phillipe Loher,et al.  Nuclear and mitochondrial tRNA-lookalikes in the human genome , 2014, Front. Genet..

[5]  Yi Jing,et al.  Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity , 2015, Nucleic acids research.

[6]  Jordan Anaya,et al.  Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets , 2014, BMC Biology.

[7]  Xavier Estivill,et al.  A highly expressed miR-101 isomiR is a functional silencing small RNA , 2013, BMC Genomics.

[8]  N. Polacek,et al.  Slicing tRNAs to boost functional ncRNA diversity , 2013, RNA biology.

[9]  Megumi Shigematsu,et al.  Transfer RNA as a source of small functional RNA. , 2014, Journal of molecular biology and molecular imaging.

[10]  Alok Bhattacharya,et al.  Analysis of the microRNA transcriptome and expression of different isomiRs in human peripheral blood mononuclear cells , 2013, BMC Research Notes.

[11]  Aristotelis Tsirigos,et al.  Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Phillipe Loher,et al.  IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies , 2014, Oncotarget.

[13]  G. Hutvagner,et al.  Transfer RNA‐derived fragments: origins, processing, and functions , 2011, Wiley interdisciplinary reviews. RNA.

[14]  Praveen Sethupathy,et al.  Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C , 2015, Scientific Reports.

[15]  Yi Jing,et al.  Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies , 2015, Oncotarget.