Letter abstract
Nature Genetics 40, 351 - 355 (2008)
Published online: 17 February 2008 | doi:10.1038/ng.73
The birth and death of microRNA genes in Drosophila
Jian Lu1, Yang Shen2, Qingfa Wu3, Supriya Kumar1, Bin He1, Suhua Shi2, Richard W Carthew4, San Ming Wang3 & Chung-I Wu1,2
MicroRNAs (miRNAs) are small, endogenously expressed RNAs that regulate mRNAs post-transcriptionally. The class of miRNA genes, like other gene classes, should experience birth, death and persistence of its members. We carried out deep sequencing of miRNAs from three species of Drosophila, and obtained 107,000 sequences that map to no fewer than 300 loci that were not previously known. We observe a large class of miRNA genes that are evolutionarily young, with a rate of birth of 12 new genes per million years (Myr). Most of these new miRNAs originated from non-miRNA sequences. Among the new genes, we estimate that 96% disappeared quickly in the course of evolution; only 4% of new miRNA genes were retained by natural selection. Furthermore, only 60% of these retained genes became integrated into the transcriptome in the long run (60 Myr). This small fraction (2.5%) of surviving miRNAs may later on become moderately or highly expressed. Our results suggest that there is a high birth rate of new miRNA genes, accompanied by a comparably high death rate. The estimated net gain of long-lived miRNA genes, which is not strongly affected by either the depth or the breadth (number of tissues) of sequencing, is 0.3 genes per Myr in Drosophila.
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA.
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou, 510275, China.
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, Evanston Northwestern Healthcare Research Institute, Northwestern University Feinberg School of Medicine, Evanston, Illinois 60208, USA.
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA.
Correspondence to: Chung-I Wu1,2 e-mail: ciwu@uchicago.edu
Correspondence to: San Ming Wang3 e-mail: swang1@northwestern.edu
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