Development Genes and Evolution

, Volume 217, Issue 1, pp 73–77 | Cite as

Evidence for a microRNA expansion in the bilaterian ancestor

  • Simon E. Prochnik
  • Daniel S. Rokhsar
  • A. Aziz Aboobaker
Sequence Corner


Understanding how animal complexity has arisen and identifying the key genetic components of this process is a central goal of evolutionary developmental biology. The discovery of microRNAs (miRNAs) as key regulators of development has identified a new set of candidates for this role. microRNAs are small noncoding RNAs that regulate tissue-specific or temporal gene expression through base pairing with target mRNAs. The full extent of the evolutionary distribution of miRNAs is being revealed as more genomes are scrutinized. To explore the evolutionary origins of metazoan miRNAs, we searched the genomes of diverse animals occupying key phylogenetic positions for homologs of experimentally verified human, fly, and worm miRNAs. We identify 30 miRNAs conserved across bilaterians, almost double the previous estimate. We hypothesize that this larger than previously realized core set of miRNAs was already present in the ancestor of all Bilateria and likely had key roles in allowing the evolution of diverse specialist cell types, tissues, and complex morphology. In agreement with this hypothesis, we found only three, conserved miRNA families in the genome of the sea anemone Nematostella vectensis and no convincing family members in the genome of the demosponge Reniera sp. The dramatic expansion of the miRNA repertoire in bilaterians relative to sponges and cnidarians suggests that increased miRNA-mediated gene regulation accompanied the emergence of triploblastic organ-containing body plans.


MicroRNA Bilateria Post-transcriptional regulation 

Supplementary material

427_2006_116_MOESM1_ESM.xls (71 kb)
Table S1Predicted miRNAs and clusters in metazoans. Predicted miRNAs are grouped in families that contain the same seed site (bases 1–7 or 2–8). miRNAs that lie <8 kb from each other on a genomic scaffold are boxed in the same color with the cluster number shown. Possible, but more distant clusters have a “?” in the cluster column and a note. Explanation of notes column: extend length of additional genomic sequence added to 5′ and 3′ ends of predicted miRNA hairpin before refolding and new ΔG folding energy (kcal/mol); ext predicted mature miRNA sequences were extended at the 5′ and 3′ ends to the same length as the query; poor terminal struct indicates the presence of an internal loop or bulge and a 1- to 2-bp stem before the main terminal loop; nonparsimonious miRNAs that have been predicted but appear to be nonparsimonious as they only have restricted homology to otherwise vertebrate specific miRNAs and are thus likely false positives and are not shown in Fig. 1 (XLS 72 kb).


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Simon E. Prochnik
    • 1
  • Daniel S. Rokhsar
    • 1
    • 2
  • A. Aziz Aboobaker
    • 2
    • 3
  1. 1.DOE Joint Genome InstituteWalnut CreekUSA
  2. 2.Center for Integrative Genomics, Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyUSA
  3. 3.Institute of GeneticsUniversity of Nottingham, Queens Medical CentreNottinghamUK

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