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.
Highlights
Transposable elements (TEs) as important components of many genomes are able to mobilize and replicate in the host genomes [1]
Identification of miRNAs derived from TEs in human and seven other vertebrates 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)
The MDTEs account for 19.84% of miRNAs in Homo sapiens and TE sequences make up 44.83% of its genome [30]
Summary
Transposable elements (TEs) as important components of many genomes are able to mobilize and replicate in the host genomes [1]. The retrotransposons can be further classified into three categories: long terminal repeat (LTR), long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE). TEs were claimed to be an evolutionary force and were found to be related to epigenetic regulatory mechanisms [3,4,5]. The discovery of small RNA led to an emerging of prospect for uncovering the functions of TEs. Various small RNAs have been discovered, such as microRNAs (miRNAs), short interfering RNAs, piwi interacting RNAs and so on [8,9,10]. MiRNA is the first discovered small RNA [10]. Most miRNAs regulate gene expression by targeting mRNA-specific regions
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