Abstract
Natural antisense transcript-derived small interfering RNAs (nat-siRNAs) are a class of functional small RNA (sRNA) that have been found in both plant and animals kingdoms. In plants, these sRNAs have been shown to suppress the translation of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex (RISC) to their sequence-specific mRNA target(s). Current computational tools for classification of nat-siRNAs are limited in number and can be computationally infeasible to use. In addition, current methods do not provide any indication of the function of the predicted nat-siRNAs. Here, we present a new software pipeline, called NATpare, for prediction and functional analysis of nat-siRNAs using sRNA and degradome sequencing data. Based on our benchmarking in multiple plant species, NATpare substantially reduces the time required to perform prediction with minimal resource requirements allowing for comprehensive analysis of nat-siRNAs in larger and more complex organisms for the first time. We then exemplify the use of NATpare by identifying tissue and stress specific nat-siRNAs in multiple Arabidopsis thaliana datasets.
Highlights
Natural antisense transcripts (NATs) are endogenous RNA transcripts that share sequence complementary to other RNA transcript sequences [1]
For each of the upregulated nat-small interfering RNA (siRNA) identified in the treatment datasets, we examined the current annotation model (TAIR10) and found that 10 of the 29 sequences originated from a NAT pair where one of the transcripts is currently annotated as a potential natural antisense gene
Small RNAs that originate from endogenous RNA transcripts that share sequence complementary to other RNA transcript sequences are termed nat-siRNAs, and like miRNAs, they have been shown to regulate the translation of specific messenger RNAs (mRNAs) through mRNA cleavage [5]
Summary
Natural antisense transcripts (NATs) are endogenous RNA transcripts that share sequence complementary to other RNA transcript sequences [1]. They have been identified in multiple eukaryotes, including humans, mice, yeast, rice and Arabidopsis [2]. NATs include both protein coding and, mostly, non-protein coding transcripts [3] and can be classified into either cis-NATs or trans-NATs based on their genomic origin. Cis-NATs are transcribed from the same genomic location but on opposite strands, resulting in sections of perfectly complementary double stranded RNA (dsRNA) forming between the two transcript sequences. Trans-NATs originate from different genomic locations and can form imperfect dsRNA [2]. Current understanding is limited, research has suggested a variety of regulatory roles for NATs, such as RNA interference (RNAi), alternative splicing, genomic imprinting, and X-chromosome inactivation [2,4,5]
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