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Molecular Biology Reports

, Volume 37, Issue 7, pp 3575–3581 | Cite as

Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus

  • Guiming Liu
  • Yongjun Fang
  • Hongming Zhang
  • Yan Li
  • Xingang Li
  • Jun Yu
  • Xumin Wang
Article

Abstract

MicroRNAs (miRNAs) belong to a class of small non-coding RNAs that play important roles in complex biological processes through degradation of target mRNAs or repression of their translation. We exploited cross-species comparison to predict miRNAs and identified 266 genes encoding 274 mature miRNAs in Oryctolagus cuniculus. Comparative analyses among mammalian genomes demonstrated that most of the identified miRNAs and their clusters are ancient in origin and conserved among mammals but a few clades as well as some species-specific miRNAs exhibit an ongoing evolutionary process where gain and loss of individual miRNAs have occurred through tandem duplications and random mutations. Our microarray- and RT–PCR-based analyses and target prediction reveal specific expression patterns in brain, spleen, muscle, heart, and ovary, and significant over-representations in certain GO categories as regarded to their mRNA targets include genes that play key roles in signal transduction and transcriptional regulation.

Keywords

MicroRNA Oryctolagus cuniculus RT–PCR Target 

Abbreviations

RISC

RNA-induced silencing complex

TE

Transposable elements

Notes

Acknowledgments

This work was supported by the National Natural Science Foundation of China (NSFC) (No. 0606035). We thank Baohong Zhang of East Carolina University for critical evaluation of the manuscrip.

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Guiming Liu
    • 1
    • 2
  • Yongjun Fang
    • 1
    • 2
  • Hongming Zhang
    • 3
  • Yan Li
    • 2
  • Xingang Li
    • 2
  • Jun Yu
    • 1
    • 2
  • Xumin Wang
    • 2
  1. 1.James D. Watson Institute of Genome SciencesZhejiang UniversityHangzhouChina
  2. 2.CAS Key Laboratory of Genome Sciences and InformationBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
  3. 3.School of Life ScienceEast China Normal UniversityShanghaiChina

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