Takane et al. BMC Genomics 2010, 11:101 http://www.biomedcentral.com/1471-2164/11/101 Page 7 of 13 Table 3 Evolutionarily conserved genes regulated by miRNAs Target gene ID Name Function Candidates targeted by multiple miRNAs ENSG00000095203 EPB41L4B Band 4.1-like protein 4B Candidates targeted by single miRNAs ENSG00000187772 LIN28B Lin-28 homolog B + ENSG00000198799 LRIG2 Leucine-rich repeats and immunoglobulin-like domains protein 2 + precursor ENSG00000086544 ITPKC Inositol-trisphosphate 3-kinase C + ENSG00000196233 LCOR Ligand-dependent corepressor + ENSG00000139263 LRIG3 Leucine-rich repeats and immunoglobulin-like domains protein 3 + precursor ENSG00000134698 EIF2C4 Eukaryotic translation initiation factor 2C 4 + ENSG00000170456 DENND5B MGC24039 protein + ENSG00000136231 IGF2BP3 Insulin-like growth factor 2 mRNA-binding protein 3 + ENSG00000158710 TAGLN2 Transgelin-2 ENSG00000143549 TPM3 Tropomyosin alpha-3 chain ENSG00000117519 CNN3 Calponin-3 ENSG00000071073 MGAT4A Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase A ENSG00000161813 LARP4 La-related protein 4 ENSG00000147416 ATP6V1B2 Vacuolar ATP synthase subunit B, brain isoform ENSG00000135862 LAMC1 Laminin subunit gamma-1 precursor ENSG00000125695 STRADA STE20-related adapter protein ENSG00000131459 GFPT2 Glucosamine–fructose-6-phosphate aminotransferase ENSG00000111145 ELK3 ETS domain-containing protein Elk-3 ENSG00000151726 ACSL1 Long-chain-fatty-acid–CoA ligase 1 ENSG00000164144 ARFIP1 Arfaptin-1 ENSG00000080819 CPOX Coproporphyrinogen III oxidase, mitochondrial precursor ENSG00000138279 ANXA7 Annexin A7 ENSG00000150093 ITGB1 Integrin beta-1 precursor ENSG00000093167 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 ENSG00000116141 MARK1 Serine/threonine-protein kinase MARK1 ENSG00000166797 FAM96A Protein FAM96A ENSG00000131914 LIN28 Lin-28 homolog A ENSG00000113282 CLINT1 EPN4_HUMAN Isoform 2 of Q14677 - Homo sapiens ENSG00000137872 SEMA6D Semaphorin-6D precursor List of conserved targets regulated by conserved miRNAs. Transcript of Band 4.1-like protein 4B is only regulated by two miRNAs (miR-1 and miR-124). “*” and “**” indicates experimentally verified miRNA-mRNA and possible miRNA-mRNA candidates revealed by microarray data, respectively. primordial regulatory relationships between miRNAs and their target genes during the early stage of bilaterian evolution. Possible regulation of evolutionarily conserved miRNA targets in bilaterian animals To provide further insight into the primary functions of evolutionarily conserved miRNAs (Table 3), we next focused on the functions of the target genes and found that evolutionarily conserved miRNA/target genes could be largely classified into four functional categories: development, differentiation, muscle movement, and gene regulation. First, we describe the function of evolu- tionarily conserved genes involved in development and differentiation. The laminin subunit gamma-1 precursor (LAMC1) gene, which was possibly regulated by miR- 124, is one of the major components of the basement membrane. According to Smyth et al. [29], muta- tion of LAMC1 causes embryonic lethality because of the absence of the basement membrane and failure to differentiate the endoderm. Among other candidates regulated by miR-124, the expression of the leucine-rich repeat flightless-interacting protein 2 (LRRFIP2) gene induces an extra axis in Xenopus laevis embryos [30]. let- miR- miR- 7 1 124 miR-125/ lin4 miR- 34 +** + +* +* + + + + +* + + + + +** + + +** + + + +* + +