Computational Approaches to tRNA-Derived Small RNAs.

Wei-Lin Xu,Ling-Ling Zheng,Yi-Dan Wang,Liang-Hu Qu,Ye Yang

doi:10.3390/ncrna3010002

Wei-Lin Xu, Ling-Ling Zheng + Show 3 more

Open Access

https://doi.org/10.3390/ncrna3010002

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Journal: Non-coding RNA	Publication Date: Jan 4, 2017
Citations: 20	License type: CC BY 4.0

Affiliation: Sun Yat-sen University

Abstract

tRNA-derived small RNAs (tDRs) are a group of small, non-coding RNAs derived from transfer RNAs (tRNAs). They can be classified as tRNA halves and tRNA-derived small RNA fragments (tRFs). Accumulating experimental evidence suggests their functional roles in cells and in various biological processes. Advances in next-generation sequencing (NGS) techniques allow a large amount of small RNA deep-sequencing data to be generated. To investigate tDRs from these data, software to identify tDRs and databases to retrieve or manage tDR data have been devised. In this review, we summarized the tools and databases for tDR identification and collection, with the aim of helping researchers choose the best tools for their analysis and inspiring the invention or improvement of tools in the field.

Highlights

The last decade witnessed the discovery of an enormous number of transfer RNAs (tRNAs)-derived small RNAs in almost all branches of life [1,2,3,4,5,6,7,8,9,10,11,12]
TDRs are classified as tRNA halves and tRNA-derived small RNA fragments. tRNA halves are generated by a single cleavage at the anticodon of mature tRNAs, and their lengths range from 30 nt to 35 nt [1]
Computational approaches aimed at assisting researchers with these steps arose, and the following is a general review of the tools and databases for tRNA-derived small RNAs (tDRs)

Summary

Introduction

The last decade witnessed the discovery of an enormous number of tRNA-derived small RNAs (tDRs) in almost all branches of life [1,2,3,4,5,6,7,8,9,10,11,12]. TRFs, are generated from both precursor (pre-tRNAs) and mature tRNAs through Dicer-dependent or -independent processes, and are approximately 20 nt in size. This classification of tDRs is not definite. Leader-exon tRNA fragment type was discovered to be associated with the loss of spinal motor neurons in CLP1-kinase dead mice [30,33] These fragments straddle the 5’ leader sequence of pre-tRNAs and the 5’ end of mature tRNAs. The mechanism of the tRF regulation of gene expression remains elusive. A more recent study revealed the existence of conserved tDRs in Arabidopsis thaliana, Oryza sativa and Physcomitrella patens [45]

Identifying tDRs and Managing tDR Data

Identifying tDRs

Databases of tDRs

Methods