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Kim Y.-J.,Dankook University | Kim Y.-J.,DKU Theragen Institute for NGS Analysis DTiNa
Genes and Genomics | Year: 2014

Transposable elements (TEs) are interspersed in the host genomic regions, and induce various effects to the host. Recent study shows TE sequences can provide microRNA (miRNA) sequences which have a crucial role in the organisms by silencing target mRNAs. In this study, 14 TE-derived miRNAs were identified by overlapping >50 % with expressed sequence tag. Among them, miR-330, miR-648, miR-1254, and miR-1825 were examined regarding their expression patterns and evolutionary conservation in various species. MiR-330 and miR-648 were highly expressed in the bone marrow and cerebellum tissues, while miR-1825 showed high expression in the fetal liver tissue. Additionally, MiR-1254 showed dominant expression in the skeletal muscle. These TE-derived miRNAs showed an inhibitory effect on the expression of their target genes, MLL2 and ARHGEF12. These findings confirmed that TEs play important roles to regulate gene expression by providing miRNA sequences and they may contribute to the evolution of biological complexity in human genome. © 2014, The Genetics Society of Korea and Springer-Science and Media.

Jun J.,Personal Genomics Institute | Cho Y.S.,Personal Genomics Institute | Cho Y.S.,The Genomics Institute | Hu H.,Personal Genomics Institute | And 13 more authors.
BMC Genomics | Year: 2014

Background: The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. Results: We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. Conclusions: Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses. © 2014 Jun et al.

Lee W.,Dankook University | Mun S.,Dankook University | Mun S.,U.S. National Institutes of Health | Kang K.,Dankook University | And 3 more authors.
Gene | Year: 2015

Alu elements are the most successful short interspersed elements in primate genomes and their retrotransposition is a major source of genomic expansion. Alu elements integrate into genomic regions through target-site primed reverse transcription, which generates target site duplications (TSDs). Unexpectedly, we have identified target site triplications (TSTs) at some loci, where two Alu elements in tandem share one direct repeat. Thus, the three copies of the repeat are present. We located 212 TST loci in the human genome and examined 25 putative human-specific TST loci using PCR validation. As a result, 12 human-specific TST loci were identified. These findings suggest that unequal homologous recombination between TSDs can lead to TST. Through this mechanism, the copy number of Alu elements could have increased in primate genomes without new Alu retrotransposition events. This study provides new insight into the augmentation of Alu elements in the primate genome. © 2015 Elsevier B.V.

Kim Y.-J.,Dankook University | Kim Y.-J.,DKU Theragen Institute for NGS Analysis DTiNa | Ahn K.,Theragen Bio Institute | Gim J.-A.,Pusan National University | And 4 more authors.
Gene | Year: 2015

Segmental duplication, or low-copy repeat (LCR) event, occurs during primate evolution and is an important source of genomic diversity, including gain or loss of gene function. The human chromosome 7q 11.23 is related to the William-Beuren syndrome and contains large region-specific LCRs composed of blocks A, B, and C that have different copy numbers in humans and different primates. We analyzed the structure of POM121, NSUN5, FKBP6, and TRIM50 genes in the LCRs of block C. Based on computational analysis, POM121B created by a segmental duplication acquired a new exonic region, whereas NSUN5B (NSUN5C) showed structural variation by integration of HERV-K LTR after duplication from the original NSUN5 gene. The TRIM50 gene originally consists of seven exons, whereas the duplicated TRIM73 and TRIM74 genes present five exons because of homologous recombination-mediated deletion. In addition, independent duplication events of the FKBP6 gene generated two pseudogenes at different genomic locations. In summary, these clustered genes are created by segmental duplication, indicating that they show dynamic evolutionary events, leading to structure variation in the primate genome. © 2015 Elsevier B.V.

Mun S.,Dankook University | Mun S.,DKU Theragen Institute for NGS Analysis DTiNa | Lee J.,Dankook University | Lee J.,University of Florida | And 5 more authors.
PLoS ONE | Year: 2014

Endogenous retroviruses (ERVs), eukaryotic transposable elements, exist as proviruses in vertebrates including primates and contribute to genomic changes during the evolution of their host genomes. Many studies about ERVs have focused on the elements residing in the human genome but only a few studies have focused on the elements which exist in non-human primate genomes. In this study, we identified 256 chimpanzee-specific endogenous retrovirus copies (PtERVs: Pan troglodyte endogenous retroviruses) from the chimpanzee reference genome sequence through comparative genomics. Among the chimpanzee-specific ERV copies, 121 were full-length chimpanzee-specific ERV elements while 110 were chimpanzee-specific solitary LTR copies. In addition, we found eight potential retrotransposition-competent full-length chimpanzee-specific ERV copies containing an intact env gene, and two of them were polymorphic in chimpanzee individuals. Through computational analysis and manual inspection, we found that some of the chimpanzee-specific ERVs have propagated via non-classical PtERV insertion (NCPI), and at least one of the PtERVs may have played a role in creating an alternative transcript of a chimpanzee gene. Based on our findings in this study, we state that the chimpanzee-specific ERV element is one of the sources of chimpanzee genomic variations, some of which might be related to the alternative transcripts in the chimpanzee population. © 2014 Mun et al.

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