Interrogation of rabbit miRNAs and their isomiRs |
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| Authors: | Li Sung-Chou Liao Yu-Lun Chan Wen-Ching Ho Meng-Ru Tsai Kuo-Wang Hu Ling-Yueh Lai Chun-Hung Hsu Chun-Nan Lin Wen-chang |
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| Institution: | aInstitute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan;bBioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan;cInstitute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan;dInstitute of Information Sciences, Academia Sinica, Taipei, Taiwan;eDepartment of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan;fInformation Sciences Institute, University of Southern California, Marina del Rey, CA, USA |
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| Abstract: | Rabbit (Oryctolagus cuniculus) is the only lagomorph animal of which the genome has been sequenced. Establishing a rabbit miRNA resource will benefit subsequent functional genomic studies in mammals. We have generated small RNA sequence reads with SOLiD and Solexa platforms to identify rabbit miRNAs, where we identified 464 pre-miRNAs and 886 mature miRNAs. The brain and heart miRNA libraries were used for further in-depth analysis of isomiR distributions. There are several intriguing findings. First, several rabbit pre-miRNAs form highly conserved clusters. Second, there is a preference in selecting one strand as mature miRNA, resulting in an arm selection preference. Third, we analyzed the isomiR expression and validated the expression of isomiR types in different rabbit tissues. Moreover, we further performed additional small RNA libraries and defined miRNAs differentially expressed between brain and heart. We conclude also that isomiR distribution profiles could vary between brain and heart tissues. |
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| Keywords: | Abbreviations: miRNA microRNA SVM support vector machine |
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