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| Status |
Public on Oct 01, 2012 |
| Title |
Evolution of mammalian miRNA genes |
| Organisms |
Gallus gallus; Ornithorhynchus anatinus; Didelphis virginiana; Macaca mulatta; Homo sapiens; Mus musculus; Monodelphis domestica |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species that represent all main mammalian lineages and birds (the evolutionary outgroup), with the aim to unravel the evolution of mammalian miRNAs. Our analyses reveal an overall expansion of miRNA repertoires in mammals, with three-fold accelerated birth rates of miRNA families in placentals and marsupials, facilitated by the de novo emergence of miRNAs in host gene introns. Generally, our analyses suggest a high rate of miRNA family turnover in mammals, with many newly emerged miRNA families being lost soon after their formation. Selectively preserved mammalian miRNA families gradually evolved higher expression levels as well as altered mature sequences and target gene repertoires, and were apparently mainly recruited to exert regulatory functions in nervous tissues. However, miRNAs that originated on the X chromosome evolved high expression levels and potentially diverse functions during spermatogenesis, including meiosis, through selectively driven duplication-divergence processes. Overall, our study thus provides detailed insights into the birth and evolution of mammalian miRNA genes and the associated selective forces.
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| Overall design |
30 main samples from five adult tissues (brain, cerebellum, heart, kidney and testis) collected in six species (human, macaque, mouse, opossum, platypus and chicken) + 5 biological replicates + 3 samples from spermatogenic cells in adult mouse testis (Sertoli cells, spermatocytes and spermatids)
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| Contributor(s) |
Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H |
| Citation(s) |
23034410 |
| Submission date |
Aug 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Henrik Kaessmann |
| Organization name |
University of Lausanne
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| Department |
Center For Integrative Genomics
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| Lab |
Kaessmann
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| Street address |
Génopode
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (7)
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| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13766 |
Illumina Genome Analyzer IIx (Macaca mulatta) |
| GPL13797 |
Illumina Genome Analyzer IIx (Gallus gallus) |
| GPL13798 |
Illumina Genome Analyzer IIx (Ornithorhynchus anatinus) |
| GPL13799 |
Illumina Genome Analyzer IIx (Monodelphis domestica) |
| GPL16010 |
Illumina Genome Analyzer IIx (Didelphis virginiana) |
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| Samples (38)
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| Relations |
| BioProject |
PRJNA174234 |
| SRA |
SRP015370 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40499_chicken_miRNA_normalized_xp.txt.gz |
5.6 Kb |
(ftp)(http) |
TXT |
| GSE40499_human_miRNA_normalized_xp.txt.gz |
8.4 Kb |
(ftp)(http) |
TXT |
| GSE40499_macaque_miRNA_normalized_xp.txt.gz |
9.9 Kb |
(ftp)(http) |
TXT |
| GSE40499_mouse_miRNA_normalized_xp.txt.gz |
13.2 Kb |
(ftp)(http) |
TXT |
| GSE40499_opossum_miRNA_normalized_xp.txt.gz |
10.2 Kb |
(ftp)(http) |
TXT |
| GSE40499_platypus_miRNA_normalized_xp.txt.gz |
5.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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