NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes

Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great res...

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Bibliographic Details
Published in:Scientific reports 2016-02, Vol.6 (1), p.21666-21666, Article 21666
Main Authors: Yu, Dongliang, Meng, Yijun, Zuo, Ziwei, Xue, Jie, Wang, Huizhong
Format: Article
Language:English
Subjects:
38/91
631/114/2164
631/61/212/2019
Antisense RNA
Binding sites
Dendrobium - genetics
Dendrobium - metabolism
Gene expression
Gene Expression Profiling - methods
Gene loci
Genomes
Humanities and Social Sciences
MicroRNAs
multidisciplinary
RNA, Plant - biosynthesis
RNA, Plant - genetics
RNA, Small Interfering - biosynthesis
RNA, Small Interfering - genetics
Science
Science (multidisciplinary)
siRNA
Transcription
Transcriptome - physiology
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Summary:Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip .
ISSN:2045-2322
2045-2322
DOI:10.1038/srep21666