Abstract
Identification of the target genes of microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and small interfering RNAs (siRNAs) is an important step for understanding their regulatory roles in plants. In recent years, many bioinformatics software packages based on small RNA (sRNA) high-throughput sequencing (HTS) and degradome sequencing data analysis have provided strong technical support for large-scale mining of sRNA-target pairs. However, sRNA-target regulation is achieved using a complex network of interactions since one transcript might be co-regulated by multiple sRNAs and one sRNA may also affect multiple targets. Currently used mining software can realize the mining of multiple unknown targets using known sRNA, but it cannot rule out the possibility of co-regulation of the same target by other unknown sRNAs. Hence, the obtained regulatory network may be incomplete. We have developed a new mining software, sRNATargetDigger, that includes two function modules, “Forward Digger” and “Reverse Digger”, which can identify regulatory sRNA-target pairs bidirectionally. Moreover, it has the ability to identify unknown sRNAs co-regulating the same target, in order to obtain a more authentic and reliable sRNA-target regulatory network. Upon re-examination of the published sRNA-target pairs in Arabidopsis thaliana, sRNATargetDigger found 170 novel co-regulatory sRNA-target pairs. This software can be downloaded from http://www.bioinfolab.cn/sRNATD.html.
Highlights
Small RNAs is a class of non-coding RNAs with lengths ranging from 18 to 30 nucleotides and different functions
Since the expression patterns of many small RNA (sRNA) and mRNAs were tissue-specific, we considered that this regulatory relationship was true as long as one tissue passed the “Forward Digger” or “Reverse Digger”function module
Function of “Forward Digger”: sRNAs were known, and their regulatory target genes were identified from the cDNA data set
Summary
Small RNAs (sRNAs) is a class of non-coding RNAs with lengths ranging from 18 to 30 nucleotides and different functions. Some sRNAs are complementarily matched with specific bases of the target mRNAs, resulting in cleavage and degradation of the target transcripts. This kind of regulation can negatively modulate the expression of target genes, and it plays important roles in many biological processes, such as plant growth and development, disease resistance, and stress response [1, 2]. SRNAs can be classified according to their distinct. This kind of regulation can negatively modulate the expression of target genes, and it plays important roles in many biological processes, such as plant growth and development, disease resistance, and stress response [1, 2]. sRNAs can be classified according to their distinct
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