Abstract
BackgroundMicroRNAs (miRNAs) are highly conserved small non-coding RNAs that play important regulatory roles in plants. Although many miRNA families are sequentially and functionally conserved across plant kingdoms (Dezulian et al. in Genome Biol 13, 2005), they still differ in many aspects such as family size, average length, genomic loci etc. (Unver et al. in Int J Plant Genomics, 2009).ResultsIn this study, we investigated changes of miRNA expression profiles during greening process of etiolated seedlings of Oryza sativa (C3) and Zea mays (C4) to explore conserved and species-specific characteristics of miRNAs between these two species. Futhermore, we predicted 47 and 42 candidate novel miRNAs using parameterized monocot specific miRDeep2 pipeline in maize and rice respectively. Potential targets of miRNAs comprising both mRNA and long non-coding RNA (lncRNA) were examined to clarify potential regulation of photosynthesis. Based on our result, two putative positive Kranz regulators reported by Wang et al. (2010) were predicted as potential targets of miR156. A few photosynthesis related genes such as sulfate adenylytransferase (APS3), chlorophyll a/b binding family protein etc. were suggested to be regulated by miRNAs. However, no C4 shuttle genes were predicted to be direct targets of either known or candidate novel miRNAs.ConclusionsThis study provided the comprehensive list of miRNA that showed altered expression during the de-etiolation process and a number of candidate miRNAs that might play regulatory roles in C3 and C4 photosynthesis.
Highlights
MicroRNAs are highly conserved small non-coding RNAs that play important regulatory roles in plants
Animal miRNAs tend to bind to 3′UTR regions of target transcripts while plant miRNAs follow more strict reverse complementary match with targets possessing limited number of targets compared with animal miRNAs [15]
By checking the overlap of predicted targets with C4 cycle genes, reported regulators of C4 trait and photosynthesis related genes, we identified potential miRNAs that might be related to C4 photosynthesis
Summary
MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that play important regulatory roles in plants. Many miRNA families are sequentially and functionally conserved across plant kingdoms (Dezulian et al in Genome Biol 13, 2005), they still differ in many aspects such as family size, average length, genomic loci etc. MiRNAs are about 21-nt long non-coding RNAs that regulate gene expression by binding to complementary sequences within their target mRNAs [3]. Plant miRNAs differ from animal miRNAs in many aspects. Plant miRNA genes are often located in intergenic regions while animal miRNA genes are often located in introns or coding sequences [14]. Plant and animal miRNAs have different lengths and stabilities of precursors and involve different enzymes during the process of biogenesis and regulation [2, 3]. Monocot and dicot miRNAs differ in statistical features such
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