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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.


Two patterns of Type II MDTEs.(A) Pattern I MDTEs. The MDTEs lost their TE features of the wholly overlapped type. For example, 72.60% of hsa-mir-1246 with its downstream sequence was derived from 147 bp to 208 bp of MLT1M. The sequence before 147 bp has lost its TE features. (B) Pattern II MDTEs. TEs take up half of the miRNAs from their head or tail. For example, the 3’ arm of hsa-mir-885 with its downstream sequence is derived from 2 bp to 192 bp of AluSc. The 5’ arm is derived from non-TE sequence.
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pone.0131365.g004: Two patterns of Type II MDTEs.(A) Pattern I MDTEs. The MDTEs lost their TE features of the wholly overlapped type. For example, 72.60% of hsa-mir-1246 with its downstream sequence was derived from 147 bp to 208 bp of MLT1M. The sequence before 147 bp has lost its TE features. (B) Pattern II MDTEs. TEs take up half of the miRNAs from their head or tail. For example, the 3’ arm of hsa-mir-885 with its downstream sequence is derived from 2 bp to 192 bp of AluSc. The 5’ arm is derived from non-TE sequence.

Mentions: In UMDTEs, 51.78% miRNA belongs to Type II MDTEs which partly overlap with TEs. Type II MDTEs was found to be generated by two patterns: Pattern I in which MDTEs loss their TE sequence features from whole TE sequences, and Pattern II in which MDTEs with a part of the pre-miRNA are derived from the head or tail of TEs (Fig 4). In Pattern I, it is evident to observe MDTEs in miRNA homologies or multi-copy miRNAs obviously. The overlap between TEs and MDTEs in pattern I is reduced from 100% to 30% or even less (Table 2).


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)

Two patterns of Type II MDTEs.(A) Pattern I MDTEs. The MDTEs lost their TE features of the wholly overlapped type. For example, 72.60% of hsa-mir-1246 with its downstream sequence was derived from 147 bp to 208 bp of MLT1M. The sequence before 147 bp has lost its TE features. (B) Pattern II MDTEs. TEs take up half of the miRNAs from their head or tail. For example, the 3’ arm of hsa-mir-885 with its downstream sequence is derived from 2 bp to 192 bp of AluSc. The 5’ arm is derived from non-TE sequence.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131365.g004: Two patterns of Type II MDTEs.(A) Pattern I MDTEs. The MDTEs lost their TE features of the wholly overlapped type. For example, 72.60% of hsa-mir-1246 with its downstream sequence was derived from 147 bp to 208 bp of MLT1M. The sequence before 147 bp has lost its TE features. (B) Pattern II MDTEs. TEs take up half of the miRNAs from their head or tail. For example, the 3’ arm of hsa-mir-885 with its downstream sequence is derived from 2 bp to 192 bp of AluSc. The 5’ arm is derived from non-TE sequence.
Mentions: In UMDTEs, 51.78% miRNA belongs to Type II MDTEs which partly overlap with TEs. Type II MDTEs was found to be generated by two patterns: Pattern I in which MDTEs loss their TE sequence features from whole TE sequences, and Pattern II in which MDTEs with a part of the pre-miRNA are derived from the head or tail of TEs (Fig 4). In Pattern I, it is evident to observe MDTEs in miRNA homologies or multi-copy miRNAs obviously. The overlap between TEs and MDTEs in pattern I is reduced from 100% to 30% or even less (Table 2).

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.