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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.


Percentage of MDTEs and different TE families in human genome.The sum of relative percentage is 100% for each group.
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pone.0131365.g003: Percentage of MDTEs and different TE families in human genome.The sum of relative percentage is 100% for each group.

Mentions: Compared to frequencies of TE families in human genome, TE families show different contributions to human MDTEs (Pearson's Chi-squared test: χ2 = 49.65, P = 1.69e-8, Fig 3). Consistent with the result of previous work [23], MIR (SINE) and DNA elements including TcMar and hAT families contribute more to origin of miRNAs compared to their frequencies in human genome. In comparison, Alu (SINE), L1 (LINE) and ERV1 (LTR) families less overlap with miRNAs. Unexpectedly, ERVL (LTR) family shows more overlap than expected regarding its frequency in human genome.


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)

Percentage of MDTEs and different TE families in human genome.The sum of relative percentage is 100% for each group.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131365.g003: Percentage of MDTEs and different TE families in human genome.The sum of relative percentage is 100% for each group.
Mentions: Compared to frequencies of TE families in human genome, TE families show different contributions to human MDTEs (Pearson's Chi-squared test: χ2 = 49.65, P = 1.69e-8, Fig 3). Consistent with the result of previous work [23], MIR (SINE) and DNA elements including TcMar and hAT families contribute more to origin of miRNAs compared to their frequencies in human genome. In comparison, Alu (SINE), L1 (LINE) and ERV1 (LTR) families less overlap with miRNAs. Unexpectedly, ERVL (LTR) family shows more overlap than expected regarding its frequency in human genome.

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.