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The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human.

Qin S, Jin P, Zhou X, Chen L, Ma F - PLoS ONE (2015)

Bottom Line: In addition, we found that the proportions of miRNAs derived from TEs (MDTEs) in human are more than other vertebrates especially non-mammal vertebrates.Furthermore, we classified MDTEs into three types and found that TE head or tail sequences along with adjacent genomic sequences contribute to generation of human miRNAs.Our current study will improve the understanding of origin and evolution of human miRNAs.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China.

ABSTRACT
MicroRNAs (miRNAs) are crucial regulators of gene expression at the post-transcriptional level in eukaryotes via targeting gene 3'-untranslated regions. Transposable elements (TEs) are considered as natural origins of some miRNAs. However, what miRNAs are and how these miRNAs originate and evolve from TEs remain unclear. We identified 409 TE-derived miRNAs (386 overlapped with TEs and 23 un-overlapped with TEs) which are derived from TEs in human. This indicates that the TEs play important roles in origin of miRNAs in human. In addition, we found that the proportions of miRNAs derived from TEs (MDTEs) in human are more than other vertebrates especially non-mammal vertebrates. Furthermore, we classified MDTEs into three types and found that TE head or tail sequences along with adjacent genomic sequences contribute to generation of human miRNAs. Our current study will improve the understanding of origin and evolution of human miRNAs.

No MeSH data available.


The proportions of MDTEs in human and seven other vertebrates.
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pone.0131365.g001: The proportions of MDTEs in human and seven other vertebrates.

Mentions: The MDTEs were identified from human and seven other vertebrates (Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Macaca mulatta and Pan troglodytes). Surprisingly, non MDTEs were found in Xenopus tropicalis. Proportions of MDTEs in miRNAs increased with the evolution of vertebrates and the proportion in human was more than those in other analyzed vertebrates (Fig 1). Meanwhile, it was observed the proportions of MDTEs in miRNAs bear little relevance to the proportions of TEs in genomes. For example, although more than one-third of the genomes are made up by TEs in Danio rerio and Xenopus tropicalis [31, 32], the proportions of MDTEs in miRNAs are less than 5%. In comparison, TE sequences constitute 9% of genome in Gallus gallus, but 6.98% of miRNAs were MDTEs [33]. The MDTEs account for 19.84% of miRNAs in Homo sapiens and TE sequences make up 44.83% of its genome [30]. This observation might be due to the significant differences between the components of TEs in Danio rerio and Xenopus tropicalis and those in human and other mammals. This argument was supported, at least in part, by the observation that the major TEs are DNA types in Danio rerio and Xenopus tropicalis compared to retrotransposable elements in mammals [30–32, 34]. Given the contribution of TEs to miRNAs were negligible in Drosophila [35], MDTEs mainly present in genomes of human and other mammals. Information of MDTEs in human and seven other vertebrates was summarized and listed in Table 1.


The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human.

Qin S, Jin P, Zhou X, Chen L, Ma F - PLoS ONE (2015)

The proportions of MDTEs in human and seven other vertebrates.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482582&req=5

pone.0131365.g001: The proportions of MDTEs in human and seven other vertebrates.
Mentions: The MDTEs were identified from human and seven other vertebrates (Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Macaca mulatta and Pan troglodytes). Surprisingly, non MDTEs were found in Xenopus tropicalis. Proportions of MDTEs in miRNAs increased with the evolution of vertebrates and the proportion in human was more than those in other analyzed vertebrates (Fig 1). Meanwhile, it was observed the proportions of MDTEs in miRNAs bear little relevance to the proportions of TEs in genomes. For example, although more than one-third of the genomes are made up by TEs in Danio rerio and Xenopus tropicalis [31, 32], the proportions of MDTEs in miRNAs are less than 5%. In comparison, TE sequences constitute 9% of genome in Gallus gallus, but 6.98% of miRNAs were MDTEs [33]. The MDTEs account for 19.84% of miRNAs in Homo sapiens and TE sequences make up 44.83% of its genome [30]. This observation might be due to the significant differences between the components of TEs in Danio rerio and Xenopus tropicalis and those in human and other mammals. This argument was supported, at least in part, by the observation that the major TEs are DNA types in Danio rerio and Xenopus tropicalis compared to retrotransposable elements in mammals [30–32, 34]. Given the contribution of TEs to miRNAs were negligible in Drosophila [35], MDTEs mainly present in genomes of human and other mammals. Information of MDTEs in human and seven other vertebrates was summarized and listed in Table 1.

Bottom Line: In addition, we found that the proportions of miRNAs derived from TEs (MDTEs) in human are more than other vertebrates especially non-mammal vertebrates.Furthermore, we classified MDTEs into three types and found that TE head or tail sequences along with adjacent genomic sequences contribute to generation of human miRNAs.Our current study will improve the understanding of origin and evolution of human miRNAs.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China.

ABSTRACT
MicroRNAs (miRNAs) are crucial regulators of gene expression at the post-transcriptional level in eukaryotes via targeting gene 3'-untranslated regions. Transposable elements (TEs) are considered as natural origins of some miRNAs. However, what miRNAs are and how these miRNAs originate and evolve from TEs remain unclear. We identified 409 TE-derived miRNAs (386 overlapped with TEs and 23 un-overlapped with TEs) which are derived from TEs in human. This indicates that the TEs play important roles in origin of miRNAs in human. In addition, we found that the proportions of miRNAs derived from TEs (MDTEs) in human are more than other vertebrates especially non-mammal vertebrates. Furthermore, we classified MDTEs into three types and found that TE head or tail sequences along with adjacent genomic sequences contribute to generation of human miRNAs. Our current study will improve the understanding of origin and evolution of human miRNAs.

No MeSH data available.