microRNA target predictions in animals

In recent years, microRNAs (miRNAs) have emerged as a major class of regulatory genes, present in most metazoans and important for a diverse range of biological functions. Because

experimental identification of miRNA targets is difficult, there has been an explosion of computational target predictions. Although the initial round of predictions resulted in very diverse

results, subsequent computational and experimental analyses suggested that at least a certain class of conserved miRNA targets can be confidently predicted and that this class of targets is

large, covering, for example, at least 30% of all human genes when considering about 60 conserved vertebrate miRNA gene families. Most recent approaches have also shown that there are

correlations between domains of miRNA expression and mRNA levels of their targets. Our understanding of miRNA function is still extremely limited, but it may be that by integrating mRNA and

miRNA sequence and expression data with other comparative genomic data, we will be able to gain global and yet specific insights into the function and evolution of a broad layer of

post-transcriptional control.

Writing a perspective in a new and fast-moving field is necessarily selective on which papers are being cited. However, I would like to apologize to all authors whose papers were not

included. I also want to thank A. Stark, U. Ohler and S. Lall for a critical reading of the manuscript and helpful suggestions, and my collaborators and members of the miRNA/RNAi community

for many interesting and stimulating discussions. J. Thierry-Mieg and D. Thierry-Mieg as well as W. Majoros and U. Ohler shared unpublished data with me. Finally, I thank A. Stark and S.

Cohen for permission to use Figure 2.

Center for Comparative Functional Genomics Department of Biology, 100 Washington Square East, New York, 10003, New York, USA

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