GSBS Student Publications
GSBS Program
Biochemistry & Molecular Pharmacology
Publication Date
2015-05-24
UMMS Affiliation
RNA Therapeutics Institute; Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology
Document Type
Article
Disciplines
Biochemistry | Bioinformatics | Computational Biology | Genetics and Genomics
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.
Rights and Permissions
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI of Published Version
10.1093/nar/gkv537
Source
Nucleic Acids Res. 2015 May 24. pii: gkv537. Link to article on publisher's site
Journal/Book/Conference Title
Nucleic acids research
Related Resources
PubMed ID
26007652
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Repository Citation
Chou, Min-Te; Han, Bo W.; Hsiao, Chiung-Po; Zamore, Phillip D.; Weng, Zhiping; and Hung, Jui-Hung, "Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs" (2015). GSBS Student Publications. 1882.
https://escholarship.umassmed.edu/gsbs_sp/1882