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Series GSE40499 Query DataSets for GSE40499
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
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.
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)
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
Department Center For Integrative Genomics
Lab Kaessmann
Street address GĂ©nopode
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platforms (7)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13766 Illumina Genome Analyzer IIx (Macaca mulatta)
Samples (38)
GSM995300 main_hsa_bra
GSM995301 main_hsa_cer
GSM995302 main_hsa_hea
BioProject PRJNA174234
SRA SRP015370

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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