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, Volume 142, Issue 1, pp 109–118 | Cite as

Evolutionary comparisons of miRNA regulation system in six model organisms

  • Xiaofan Mao
  • Li Li
  • Yicheng Cao
Article

Abstract

miRNAs are a class of endogenous small non-coding regulatory RNAs, that can mediate the transcriptional gene silencing as well as gene expression activation. miRNAs, which are found in a wide range of species, participate in cell differentiation, proliferation, development, apoptosis, tumorigenesis, metabolism, immune system, and signaling pathways. Here, we focused on the relationship between evolution and the miRNA system, with an emphasis on both miRNAs and their target genes. Six species from the evolutionary ladder were selected as a focus of this study. Public data were retrieved and combined to compare miRNAs abundance, miRNA families, molecular functions of target genes, biological processes of target genes, protein families of target gene products, transcription factors regulated by the miRNAs, signaling pathways and tissues across the six species. We found that the expansion rate of miRNAs was significantly higher compared to other genes in human evolution. Newborn miRNA families, which were quantitatively larger than dead miRNA families, seem to be closely related to the species complexity and tissue specificity. Additionally, miRNAs in higher order species were more likely to target genes related to signaling and the immune system, while miRNAs from lower order species preferred to target genes related to the embryonic development process, reproduction and growth. Meanwhile, miRNA systems displayed diversity in regulating transcription factors, signaling pathways and tissues. Our research suggested that the miRNA system might promote evolution, especially in higher species.

Keywords

microRNA Evolution Target genes Model organisms 

Notes

Acknowledgments

We would like to extend our thanks to Professor Cao who directly instructed us for this research.

Conflict of interests

The authors declare no conflict of interests.

Supplementary material

10709_2014_9758_MOESM1_ESM.xlsx (29 kb)
File 1a and 1b: These files list the proportions of miRNA-target pairs of each molecular function(GO terms), which might show positive correlations (file 1a) and negative correlations (file 1b) with the evolution levels in both experiment validated data and predicted data. (XLSX 28 kb)
10709_2014_9758_MOESM2_ESM.xlsx (16 kb)
Supplementary material 2 (XLSX 15 kb)
10709_2014_9758_MOESM3_ESM.xlsx (33 kb)
File 2a and file 2b: These files list the proportions of miRNAs-target pairs of each biological process(GO terms), which might show positive correlations (file 2a) and negative correlations (file 2b) with the evolution levels in both experiment validated data and predicted data. (XLSX 32 kb)
10709_2014_9758_MOESM4_ESM.xlsx (28 kb)
Supplementary material 4 (XLSX 28 kb)
10709_2014_9758_MOESM5_ESM.xlsx (16 kb)
File 3a and file 3b: These files list the proportions of miRNAs-target pairs of each Pfam, which might show positive correlations (file 3a) and negative correlations (file 3b) with the evolution levels in both experiment validated data and predicted data. (XLSX 16 kb)
10709_2014_9758_MOESM6_ESM.xlsx (13 kb)
Supplementary material 6 (XLSX 13 kb)

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.School of Bioscience and Bioengineering, Higher Education Mega CenterSouth China University of TechnologyGuangzhouChina

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