The 5th International Tunicate Meeting
Okinawa Industry Support Center, Naha, Okinawa, Japan
June 21, 2009
Poster 6-7 (Session 6: Gene network and genomics)
Poster presentation

Genomic organization and developmental expression of tunicate microRNAs
Saori Tani1, Rie Kusakabe1, Yuki Miyamoto2, Kohji Okamura3, Kenta Nakai3, Takehiro G. Kusakabe2, and Kunio Inoue1
1Dept. Biol., Grad. Sch. Sci., Kobe Univ., 2Dept. Biol., Fac. Sci. Eng., Konan Univ., 3Inst. Med. Sci., Univ. Tokyo
MicroRNAs (miRs) are short non-coding RNA molecules of 21-25 nt long, which regulate gene expression patterns by silencing activity of specific target mRNA. Many of the miRs are shared across different animal taxa, and are expressed in conserved tissue-specific manners. It has been suggested that the dramatic expansion in variety of miRs occurred during chordate evolution.
We anticipate that expression patterns of tunicate miRs would provide insights into the functional elaboration of non-coding RNAs in chordate evolution. As the first step of the comprehensive analysis of tunicate non-coding RNAs, we searched in the Ciona genome database for the homologues of the representative miRs that have been analyzed in vertebrates. Expression patterns of identified miRs are examined by Northern blotting and whole mount in situ hybridization using locked-nucleic-acid-modified (LNA) probe.
One of our major interests is the muscle-specific miRs such as miR-1 (miR-206) and miR-133, which are closely linked in the genome. We found that both C. intestinalis and C. savignyi possess a single copy of the miR-1/miR-133 cluster, whereas vertebrates possess more than two copies. Ciona miR-1/miR-133 cluster is as compact as about 300 nt long, and located in the intron of the mindbomb gene in reverse orientation, similarly to that of vertebrates. MiR-133 is expressed during embryogenesis and in larvae, whereas no detectable expression of miR-1 is observed before metamorphosis. In adults, both miR-133 and miR-1 are expressed specifically in different muscle tissues. Our results suggest that these muscle-specific miRs are independently regulated in Ciona.