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

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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.

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Abbreviations

RISC:

RNA-induced silencing complex

TE:

Transposable elements

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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.

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Authors and Affiliations

  1. James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China

    Guiming Liu, Yongjun Fang & Jun Yu

  2. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

    Guiming Liu, Yongjun Fang, Yan Li, Xingang Li, Jun Yu & Xumin Wang

  3. School of Life Science, East China Normal University, Shanghai, China

    Hongming Zhang

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  1. Guiming Liu
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  2. Yongjun Fang
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  4. Yan Li
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  7. Xumin Wang
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Correspondence to Xumin Wang.

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Liu, G., Fang, Y., Zhang, H. et al. Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus . Mol Biol Rep 37, 3575–3581 (2010). https://doi.org/10.1007/s11033-010-0006-5

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  • DOI: https://doi.org/10.1007/s11033-010-0006-5

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