Evolution of the myosin heavy chain gene MYH14 and its intronic microRNA miR-499: muscle-specific miR-499 expression persists in the absence of the ancestral host gene.
BACKGROUND
A novel sarcomeric myosin heavy chain gene, MYH14, was identified following the completion of the human genome project. MYH14 contains an intronic microRNA, miR-499, which is expressed in a slow/cardiac muscle specific manner along with its host gene; it plays a key role in muscle fiber-type specification in mammals. Interestingly, teleost fish genomes contain multiple MYH14 and miR-499 paralogs. However, the evolutionary history of MYH14 and miR-499 has not been studied in detail. In the present study, we identified MYH14/miR-499 loci on various teleost fish genomes and examined their evolutionary history by sequence and expression analyses.


RESULTS
Synteny and phylogenetic analyses depict the evolutionary history of MYH14/miR-499 loci where teleost specific duplication and several subsequent rounds of species-specific gene loss events took place. Interestingly, miR-499 was not located in the MYH14 introns of certain teleost fish. An MYH14 paralog, lacking miR-499, exhibited an accelerated rate of evolution compared with those containing miR-499, suggesting a putative functional relationship between MYH14 and miR-499. In medaka, Oryzias latipes, miR-499 is present where MYH14 is completely absent in the genome. Furthermore, by using in situ hybridization and small RNA sequencing, miR-499 was expressed in the notochord at the medaka embryonic stage and slow/cardiac muscle at the larval and adult stages. Comparing the flanking sequences of MYH14/miR-499 loci between torafugu Takifugu rubripes, zebrafish Danio rerio, and medaka revealed some highly conserved regions, suggesting that cis-regulatory elements have been functionally conserved in medaka miR-499 despite the loss of its host gene.


CONCLUSIONS
This study reveals the evolutionary history of the MYH14/miRNA-499 locus in teleost fish, indicating divergent distribution and expression of MYH14 and miR-499 genes in different teleost fish lineages. We also found that medaka miR-499 was even expressed in the absence of its host gene. To our knowledge, this is the first report that shows the conversion of intronic into non-intronic miRNA during the evolution of a teleost fish lineage.
Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan. akino@mail.ecc.u-tokyo.ac.jp.
Sharmin Siddique
SS
Bhuiyan
Shigeharu
S
Kinoshita
Chaninya
C
Wongwarangkana
Md
M
Asaduzzaman
Shuichi
S
Asakawa
Shugo
S
Watabe
D000818:Animals; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics*; D005399:Fishes / Q000145:classification / Q000235:genetics*; D006801:Humans; D007438:Introns; D008322:Mammals / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D018995:Myosin Heavy Chains / Q000235:genetics*; D024462:Myosin Type II / Q000235:genetics; D009990:Oryzias / Q000235:genetics; D010802:Phylogeny; D026801:Synteny; D015027:Zebrafish / Q000235:genetics
D029941:Fish Proteins; D035683:MicroRNAs; D018995:Myosin Heavy Chains; D024462:Myosin Type II; C548683:MIRN499 microRNA, human; C477830:MYH7b protein, human