Firoz Ahmed, Patrick Xuechun Zhao
Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401, USA.


The roles of microRNAs (miRNAs) in gene regulation have been well recognized. Recent establishment of large-scale high-throughput small RNA sequencing projects, such as the deepBase project (, showed that along with the annotated mature miRNA several isomeric sequences are also generating from the same hairpin pre-miRNA. These isomers featuring slight variation at terminal sequence of the annotated matured miRNA, arise due to variation in site of cleavage by DCL (Dicer-Like enzyme) and thus making a pool of isomiRs. A systematic analysis was carried out to investigate isomiRs of Arabidopsis thaliana retrieved from the deepBase database. Several characteristics of isomiRs were observed. Our initial results suggested that 5p and 3p arms of miRNA precursors having equal potential to generate mature sequence. We observed that most preferred length of matured sequence is 21 nt long covering more than 50% in all studied isomiRs. Furthermore, analysis of sequence motif at the terminal of isomiRs revealed prevalence of U-rich motifs at 5′-end while A-rich motif at 3′-end. Accuracy of cleavage by DCL to generate 5′- and 3′-end of each miRNA were also analyzed and found that the cleavage at 5′-end are more precise than that of 3′-end. In order to further study the biological role of these isomiRs, we predicted the targets using the psRNATarget web server ( and obtained reliable miRNA:target lists. Interestingly, we observed that some genes are commonly targeted by several members of isomiRs, while most genes are not, an overlooked phenomenon where different transcript was targeted by slight variation of miRNA sequence. This study will provide more insights about miRNAs biogenesis and also help to unravel their most reliable target genes. Furthermore, such feature associated with miRNA may be implemented for rational design of artificial miRNA/shRNA for more potent gene silencing.   Read More …

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