title: Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves.
abstract: BACKGROUND
  MicroRNAs (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).
  
  
  RESULTS
  In 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 C4shuttle genes were predicted to be direct targets of either known or candidate novel miRNAs.
  
  
  CONCLUSIONS
  This 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 C3and C4photosynthesis.
authors.affiliation: Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Jiajia
authors.initials: J
authors.lastname: Xu
authors.affiliation: Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Yaling
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China. zhuxinguang@picb.ac.cn.|State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China. zhuxinguang@picb.ac.cn.
authors.forename: Xin-Guang
authors.initials: XG
authors.lastname: Zhu
mesh_terms: D064527:Etiolation / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D035683:MicroRNAs / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*
chemical_list: D035683:MicroRNAs