title: Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs.
abstract: Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3' end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor.
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China.
authors.forename: Min-Te
authors.initials: MT
authors.lastname: Chou
authors.affiliation: RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Bo W
authors.initials: BW
authors.lastname: Han
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China.
authors.forename: Chiung-Po
authors.initials: CP
authors.lastname: Hsiao
authors.affiliation: RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Phillip D
authors.initials: PD
authors.lastname: Zamore
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China juihunghung@gmail.com jhhung@nctu.edu.tw.
authors.forename: Jui-Hung
authors.initials: JH
authors.lastname: Hung
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry*; D034741:RNA, Small Interfering / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D015027:Zebrafish / Q000235:genetics
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering