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Evolutionary relationships between miRNA genes and their activity

Yan Zhu3, Geir Skogerbø2, Qianqian Ning1, Zhen Wang1, Biqing Li1, Shuang Yang4, Hong Sun12* and Yixue Li12*

Author affiliations

1 Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

2 Shanghai Center for Bioinformation Technology, Shanghai, 200235, China

3 Department of Cardiology, Gansu Provincial Hospital, Lanzhou, 730000, China

4 School of Life Science and Technology, Tongji University, Shanghai, 200092, China

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Citation and License

BMC Genomics 2012, 13:718  doi:10.1186/1471-2164-13-718

Published: 22 December 2012



The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained.


In order to systematically understand the evolutionary relationship between miRNAs gene and their function, we classified human known miRNAs into eight groups based on their evolutionary ages estimated by maximum parsimony method. New miRNA genes with new functional sequences accumulated more dynamically in vertebrates than that observed in Drosophila. Different levels of evolutionary selection were observed over miRNA gene sequences with different time of origin. Most genic miRNAs differ from their host genes in time of origin, there is no particular relationship between the age of a miRNA and the age of its host genes, genic miRNAs are mostly younger than the corresponding host genes. MicroRNAs originated over different time-scales are often predicted/verified to target the same or overlapping sets of genes, opening the possibility of substantial functional redundancy among miRNAs of different ages. Higher degree of tissue specificity and lower expression level was found in young miRNAs.


Our data showed that compared with protein coding genes, miRNA genes are more dynamic in terms of emergence and decay. Evolution patterns are quite different between miRNAs of different ages. MicroRNAs activity is under tight control with well-regulated expression increased and targeting decreased over time. Our work calls attention to the study of miRNA activity with a consideration of their origin time.