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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.


Analysis of three types of MDTEs.(A) Three types of MDTEs. Type I Inverted—The pre-miRNA is derived from two inverted TEs. Type II Partly overlapped—One arm is a TE while the other is the complementary sequence of that TE. Part of the pre-miRNA is derived from a TE, but another part is without TE features. Type III Wholly overlapped—The pre-miRNA wholly overlaps with a TE. Genome sequence is marked with green bar, pre-miRNA with purple bar and mature miRNA with yellow bar. Red arrow indicates the direction of TE sequence. (B) Percentage of three types of MDTEs. (C) The proportion of TE families in three types of MDTEs.
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pone.0131365.g002: Analysis of three types of MDTEs.(A) Three types of MDTEs. Type I Inverted—The pre-miRNA is derived from two inverted TEs. Type II Partly overlapped—One arm is a TE while the other is the complementary sequence of that TE. Part of the pre-miRNA is derived from a TE, but another part is without TE features. Type III Wholly overlapped—The pre-miRNA wholly overlaps with a TE. Genome sequence is marked with green bar, pre-miRNA with purple bar and mature miRNA with yellow bar. Red arrow indicates the direction of TE sequence. (B) Percentage of three types of MDTEs. (C) The proportion of TE families in three types of MDTEs.

Mentions: When multi-copy MDTEs were excluded, 338 unique MDTEs (UMDTEs) were identified and can be classified into three types (Fig 2A): Type I UMDTEs derived from inverted TE sequences, Type II UMDTEs with sequences partly overlap with TE sequences that are not inverted, and Type III UMDTEs with sequences wholly overlap with TE sequences.


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)

Analysis of three types of MDTEs.(A) Three types of MDTEs. Type I Inverted—The pre-miRNA is derived from two inverted TEs. Type II Partly overlapped—One arm is a TE while the other is the complementary sequence of that TE. Part of the pre-miRNA is derived from a TE, but another part is without TE features. Type III Wholly overlapped—The pre-miRNA wholly overlaps with a TE. Genome sequence is marked with green bar, pre-miRNA with purple bar and mature miRNA with yellow bar. Red arrow indicates the direction of TE sequence. (B) Percentage of three types of MDTEs. (C) The proportion of TE families in three types of MDTEs.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4482582&req=5

pone.0131365.g002: Analysis of three types of MDTEs.(A) Three types of MDTEs. Type I Inverted—The pre-miRNA is derived from two inverted TEs. Type II Partly overlapped—One arm is a TE while the other is the complementary sequence of that TE. Part of the pre-miRNA is derived from a TE, but another part is without TE features. Type III Wholly overlapped—The pre-miRNA wholly overlaps with a TE. Genome sequence is marked with green bar, pre-miRNA with purple bar and mature miRNA with yellow bar. Red arrow indicates the direction of TE sequence. (B) Percentage of three types of MDTEs. (C) The proportion of TE families in three types of MDTEs.
Mentions: When multi-copy MDTEs were excluded, 338 unique MDTEs (UMDTEs) were identified and can be classified into three types (Fig 2A): Type I UMDTEs derived from inverted TE sequences, Type II UMDTEs with sequences partly overlap with TE sequences that are not inverted, and Type III UMDTEs with sequences wholly overlap with TE sequences.

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.