Identification and characterization of transposable elements inserted into the coding sequences of horse genes

안궁,배진한,김정안,이자랑,정이든,박경도,한규동,조병욱,김희수 한국유전학회 2013 Genes & Genomics Vol.35 No.4

Transposable elements (TEs) are repetitive sequences dispersed throughout mammalian genomes, and they occupy important genetic positions. TEs have been shown to have both harmful and beneficial effects such as exonization, polyadenylation, and/or altering transcription rates in various vertebrate genomes. However, to the best of our knowledge, no study has yet considered the relationship between TEs and horse genes. In this study, we examined the contribution of TEs to the horse genome by collecting TEs inserted within mRNA genes. By screening the abundance,distribution, and orientation of TEs, we found that the majority of TE insertions belong to retroelements and DNA elements, most of which exist in the coding sequences of horse genes. In addition, the MIR, L1, L2, ERVL, and ERVL-MaLR subfamilies were found to be the most abundant in both non-LTR and LTR elements. Retroelements (LTRs, LINEs, and SINEs) among the TEs inserted in the coding sequences showed a preference for antisense orientation. The most pronounced imbalance in insertional orientation was observed in LINEs, which represent 40 %of all TEs in antisense orientation. Through these analyses, we identified that a total of 1310 TEs have been integrated into horse mRNA genes and small fractions of them have been exonized into coding sequences.

Structural and Quantitative Expression Analyses of HERV Gene Family in Human Tissues

안궁,김희수 한국분자세포생물학회 2009 Molecules and cells Vol.28 No.2

Human endogenous retroviruses (HERVs) have been implicated in the pathogenesis of several human diseases as multi-copy members in the human genome. Their gene expression profiling could provide us with important insights into the pathogenic relationship between HERVs and cancer. In this study, we have evaluated the genomic structure and quantitatively determined the expression patterns in the env gene of a variety of HERV family members located on six specific loci by the RetroTector 10 program, as well as real-time RT-PCR amplification. The env gene transcripts evidenced significant differences in the human tumor/normal adjacent tissues (colon, liver, uterus, lung and testis). As compared to the adjacent normal tissues, high levels of expression were noted in testis tumor tissues for HERV-K, in liver and lung tumor tissues for HERV-R, in liver, lung, and testis tumor tissues for HERV-H, and in colon and liver tumor tissues for HERV-P. These data warrant further studies with larger groups of patients to develop biomarkers for specific human cancers.

Identification of reference genes for normalization of gene expression in thoroughbred and Jeju native horse(Jeju pony) tissues

안궁,Jin-Han Bae,남규휘,Chong-Eon Lee,박경도,이학교,조병욱,김희수 한국유전학회 2011 Genes & Genomics Vol.33 No.3

Quantitative analysis of horse gene expression profiles under diverse experimental conditions is limited by the lack of reliable reference genes for normalization of mRNA levels. Therefore, in this study, the expression of potential reference genes was compared between thoroughbred and Jeju native horse (Jeju pony). We compared the expression of nine genes by quantitative real-time RT-PCR in fourteen tissues between the two horse breeds and analyzed their stability using the geNorm and NormFinder programs. The data obtained in this study suggest that the UBB gene could serve as a reference gene in gene expression analysis of thoroughbred and Jeju native horses.

Quantitative analysis of the HERV pol gene in human tissues

안궁,한규동,김희수 한국유전학회 2011 Genes & Genomics Vol.33 No.4

Human endogenous retroviruses (HERVs) have been associated with cancer pathogenesis due to their close homology to exogenous tumorigenic retroviruses. The expression pattern of HERVs could provide important insights into the pathogenic state between HERVs and various cancers. Using the RetroTector10 program, we identified four full-length HERV elements (HML4, HERV-T, HERV-F, and HERV-R) that contain pol genes with reverse transcriptase sub domains. Through a quantitative real-time RT-PCR approach, we investigated expression levels of their pol genes in various human tissues including tumor and adjacent normal tissue samples. The HML4 and HERV-T pol genes were ubiquitously expressed in all human tissues, whereas the HERV-F pol gene was only expressed in the human placenta. In further analysis, we compared expression levels of the HERV pol genes in normal tissues and their corresponding tumor tissues. Interestingly, the HERV-F pol gene showed high expression in lung tumors while its expression level was very low in normal lung tissues (p-value = 0.007). In addition, the HERV-R pol gene showed a higher expression in stomach tumors than in normal tissues (p-value = 0.044). Thus, we suggest that the expression profiling of HERV-F and HERV-R pol genes could be used as a molecular marker system to detect human stomach and lung cancers, respectively.

mRNA sequence analysis and quantitative expression of the ADAMTS4 gene in the thoroughbred horse

문재우,안궁,배진한,남규휘,조병욱,박경도,이학교,양영목,김태훈,성환후,한규동,김희수 한국유전학회 2012 Genes & Genomics Vol.34 No.4

Cartilage increases flexibility of motion and helps protect the body from physical shock. Strong physical shock or some biological factor could cause joint disease. ADAMTS4 (a disintegrin and metalloproteinase with thrombospondin motifs 4)has been related to degradation of aggrecans in cartilage. It has been associated with joint disease, which could influence the ability of horses to exercise. Here, we performed sequence analysis and expression profiling of the ADAMTS4 gene in thoroughbred horses. Quantitative real-time RT-PCR data indicated that higher expression of the ADAMTS4 gene appeared in the cartilage tissues compared to those of pancreas, stomach,lung and colon. The expression pattern was also higher in the muscle tissues after exercise than before exercise. These data could be of great use for further studies in relation to both horse racing and joint disease.

운동과 장내 미생물: 연구방법의 발전과 연구동향

백경완,안궁,안용주,XIANG YINGYING,김지석 한국운동생리학회 2022 운동과학 Vol.31 No.4

PURPOSE: To suggest future research directions and current research trends based on representative studies of existing exercises and the gut microbiome. In addition, we reviewed methodologies to study the relationship between exercise and the gut microbiome. METHODS: The research methodologies and results were integrated through a literature review of the latest “exercise and gut microbiome” studies and a narrative review. RESULTS: Although exercise is indirectly related to the gut microbiome or immunity, evidence for a direct effect is still lacking. However, with the recent discovery of gut microbiomes that can help improve exercise performance, it is clear that exercise can positively alter the gut microbiome. CONCLUSIONS: Strong evidence suggests that regular moderate exercise improves overall immune function and lowers the incidence of inflammation-related disease. In addition, certain microorganisms affect exercise performance

Profiling and identification of pregnancy-associated circulating microRNAs in dairy cattle

Kesavan Markkandan,안궁,이동진,김태일,당창권,홍송의,윤호백,임현주,홍창표 한국유전학회 2018 Genes & Genomics Vol.40 No.10

Holstein is one among the dairy cattle which provide higher milk yields than most other cattle breeds. Lack of high-accuracy, reliable methods for early detection of cattle pregnancy reduces overall productivity and constitutes a high economic burden to the dairy industry. The circulating microRNAs (miRNAs) in exosomes could provide information and serve as potential biomarkers for livestock health and disease. However, the complexity of miRNA in response to cattle early pregnancy remains unknown. Hence, we collected blood samples of three healthy dairy cows of normal and 30 days of pregnancy, in order to further characterize the miRNA transcriptome profile. A high-throughput RNA-Seq approach detected 794 known and 2154 novel circulating miRNAs in six libraries. A total of 29 miRNAs in the 30 days of pregnancy group showed significant differences compared to the normal group. Further, bta-miR-450b, bta-miR-146b, bta-miR-26b and bta-miR-27b were upregulated which shown to be involved in preeclampsia, immune response and mammary gland development. GO enrichment analysis showed these target genes were involved in the metabolic process, signal transducer activity, and membrane etc., while KEGG analysis showed that these genes were enriched in membrane trafficking, chromosome and associated proteins, exosome and G protein-coupled receptors pathways. These results provide an experimental basis to reveal the potential role of miRNAs as biomarkers in early diagnosis of pregnancy and other molecular functions.

Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements

김정안,하홍석,안궁,김대수,김희수 한국유전체학회 2014 Genomics & informatics Vol.12 No.4

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) shareseveral characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novelRE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided intosix major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified asRE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

Identification and characterization of transposable element-mediated chimeric transcripts from porcine Refseq and EST databases

하홍석,문재우,김정안,정이든,안궁,오건봉,김태훈,성환후,김희수 한국유전학회 2012 Genes & Genomics Vol.34 No.4

Transposable elements are mobile genomic sequences that comprise a large portion of mammalian genomes. The transposable element fusion phenomenon within porcine genes has not yet been reported; therefore, we investigated transposable element fusion genes in the Sus scrofa genome. Porcine transposable element-mediated chimeric transcripts were identified and characterized. Most transposable elements preferentially inserted themselves into an antisense orientation and into the 3' end of porcine genes. The transposable element fusion gene between porcine mRNA and ERV class I, one of the LTR retrotransposons, was not detected. This data will be of great use to further studies focused on a better understanding of the biological function of porcine genes in relation to transposable elements.

Identification of transposable elements fused in the exonic region of the olive flounder genome

남규휘,김정안,MISHRA ANSHUMAN,안궁,김석만,김도형,차희재,최영현,박찬일,김희수 한국유전학회 2018 Genes & Genomics Vol.40 No.7

Transposable elements (TEs) are mobile genetic sequences that comprise a large portion of vertebrate genomes. The olive flounder (Paralichthys olivaceus) is a valuable marine resource in East Asia. The scope of most genomic studies on the olive flounder is limited to its immunology as their focus is the prevention of mass mortality of this species. Thus, for a broader understanding of the species, its genomic information is consistently in demand. Transcripts sequences were acquired from transcriptome analysis using gill tissues of 12 olive flounders. Distribution of TEs inserted in exonic region of the olive flounder genome was analyzed using RepeatMasker (http://www.repea tmask er.org/). We found 1140 TEs in the exonic region of the genome and long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs) insertions occurred with forward orientation preferences. Transposons belonging to the hAt, Gypsy, and LINE 1 (L1) subfamilies were the most abundant DNA transposons, LTRs, and long interspersed elements (LINEs), respectively. Finally, we carried out a gene ontology analysis to determine the function of TE-fused genes. These results provide some genomic information about TEs that is useful for future research on changes in properties and functions of genes by TEs in the olive flounder genome.