title: Interrogation of rabbit miRNAs and their isomiRs.
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.
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan. pinus@ibms.sinica.edu.tw
authors.forename: Sung-Chou
authors.initials: SC
authors.lastname: Li
authors.forename: Yu-Lun
authors.initials: YL
authors.lastname: Liao
authors.forename: Wen-Ching
authors.initials: WC
authors.lastname: Chan
authors.forename: Meng-Ru
authors.initials: MR
authors.lastname: Ho
authors.forename: Kuo-Wang
authors.initials: KW
authors.lastname: Tsai
authors.forename: Ling-Yueh
authors.initials: LY
authors.lastname: Hu
authors.forename: Chun-Hung
authors.initials: CH
authors.lastname: Lai
authors.forename: Chun-Nan
authors.initials: CN
authors.lastname: Hsu
authors.forename: Wen-chang
authors.initials: WC
authors.lastname: Lin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D020869:Gene Expression Profiling; D015723:Gene Library; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D008969:Molecular Sequence Data; D005810:Multigene Family; D011817:Rabbits / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs