Identification of the highly accumulated microRNA*s in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) |
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Authors: | Chaogang Shao Xiaoxia Ma Xiufang Xu Yijun Meng |
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Institution: | 1. College of Life Sciences, Huzhou Teachers College, Huzhou 313000, PR China;2. College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China |
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Abstract: | Plant microRNAs (miRNAs) are crucial for the regulation of gene expression, which is involved in almost all the important biological processes. In the cytoplasm, the miRNA strand is selectively incorporated into a specific Argonaute (AGO)-associated gene silencing complex, while the miRNA* is degraded rapidly. Thus, most miRNA*s were thought to be biologically meaningless. Interestingly, several recent reports in both plants and animals have shaken this notion. Many miRNA*s were demonstrated to possess regulatory roles in gene expression. However, the low accumulation levels of most miRNA*s raise the question whether the activities of this small RNA (sRNA) species are widespread in plants. Here, by using publicly available sRNA high-throughput sequencing data, we found that the accumulation levels of several miRNA*s could be much higher than those of their miRNA partners in certain organs, mutants and/or AGO-associated silencing complexes of both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Based on target prediction and degradome sequencing data-based validation, some of these highly accumulated miRNA*s were indicated to possess cleavage-based potential regulatory role on certain targets. Besides, some interesting biological interpretations were obtained based on the accumulation patterns of the miRNA*s, the annotations of the target genes, and literature mining. Taken together, the expanded list of the highly accumulated miRNA*s along with their potential target genes discovered in this study further strengthened the current notion that certain members of the miRNA* species are biologically relevant, which needs further inspection. |
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Keywords: | miRNA microRNA pri-miRNA primary microRNA pre-miRNA precursor microRNA DCL1 Dicer-like 1 AGO Argonaute miRISC microRNA-induced silencing complex sRNA small RNA HTS high-throughput sequencing TE transposable element GEO Gene Expression Omnibus CSRDB Cereal Small RNAs Database RPM reads per million RACE rapid amplification of cDNA ends TAIR the Arabidopsis information resource TIGR the institute for genome research t-plot target plot |
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