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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.
In vitro CpG methylation and garcinol reduce PERV LTR promoter activity
하홍석,이영춘,박상제,정이든,안궁,문재우,한규동,오건봉,김태헌,성환후,김희수 한국유전학회 2012 Genes & Genomics Vol.34 No.2
Porcine endogenous retroviruses (PERVs) in the pig genome represent a potential risk of infection in pig-to-human transplantation. Long terminal repeats (LTRs) are known to be strong promoter elements that could regulate the transcription activity of PERV elements. It is possible that DNA methylation controls promoter activity of PERV family. Here,we analyzed CpG dinucleotides and CpG islands of six transcribed PERV LTRs. Promoter activity of the LTRs from the six clones methylated by CpG methyltransferase (M. SssI), and luciferase assay after garcinol treatment (histone acetyltransferase inhibitor) were examined, indicating that promoter activity of the PERV LTRs was significantly decreased.
하홍석(Ha Hong-Seok),허재원(Huh Jae-Won),김대수(Kim Dae-Soo),박상제(Park Sang-Je),배진한(Bae Jin-Han),안궁(Ahn Kung),윤세은(Yun Se-Eun),김희수(Kim Heui-Soo) 한국생명과학회 2009 생명과학회지 Vol.19 No.4
유전자의 융합으로 인한 돌연변이는 염색체 재배열, 트랜스스플라이싱, 유전자간 스플라이싱으로 인하여 야기된다고 알려져 있다. 우리는 두 개의 서로 다른 유전자의 pre-mRNA의 융합으로 인하여 만들어지는 트랜스 스플라이싱의 전사 산물에 관심을 가져, 인간의 태아 줄기 세포에서 이러한 돌연변이 양상을 분석하였다. 배아줄기세포의 mRNA에서 트랜스 스플라이싱 전사체 70개를 탐지해 내고, 이들의 융합되는 패턴에 따라 5'UTR-5'UTR, 5'UTR-3'UTR, 3'UTR-3'UTR, 5'UTRCDS, 3'UTR-CDS, CDS-CDS의 6개의 유형으로 분류하여 분석하였다. 두 유전자의 융합되는 영역은 UTR영역보다 CDS에서 풍부하였는데, 이러한 이유는 많은 인트론 수로 인해 야기되는 것으로 추정된다. 융합되는 유전자의 염색체상의 위치분석 결과, 17번과 19번 염색체가 융합유전자의 활성화를 나타내었다. 이러한 연구결과는 향후 융합유전자와 인간의 질병연구에 크게 기여할 것으로 사료된다. Genetic mutations by gene fusion result from chromosomal rearrangement, trans-splicing, and intergenic splicing. Trans-splicing is a phenomenon in which two pre-mRNAs grow together into one. We analyzed the trans-splicing products in embryonic stem cells. By using bioinformatic tools, 70 trans-splicing transcripts were identified. They are classified into 6 types according to fusion pattern: 5'UTR-5'UTR, 5'UTR-3'UTR, 3'UTR-3'UTR, 5'UTR-CDS, 3'UTR-CDS, CDS-CDS. The fusion products are more abundant in CDS regions than in UTR regions, which contain multiple intron numbers. Chromosome analysis showing gene fusion via trans-splicing indicated that chromosomes 17 and 19 were activated. These data are of great use for further studies in relation to fusion genes and human diseases.
Identification and Promoter Analysis of PERV LTR Subtypes in NIH-Miniature Pig
정이든,하홍석,박상제,오근봉,임기선,김태훈,성환후,김희수 한국분자세포생물학회 2013 Molecules and cells Vol.35 No.2
Porcine endogenous retroviruses (PERVs) are integrated into the genomes of all pigs. Since some PERVs can also infect human cells, they represent a potential risk for xeno-transplantation involving pig cells or organs. The long terminal repeat (LTR) elements of PERVs show pro-moter activity that can affect human functional genes; therefore, we examined these elements in this study. We detected several expressed LTRs in the NIH-miniature pig liver, among which we identified 9 different subtypes. When these LTRs were compared, distinct structures that contained several insertion and deletion (INDEL) events and tandem repeats were identified in the U3 region. The transcriptional activity of the 9 LTR subtypes was analyzed in the PK15 porcine cell line and in the HepG2 and Hep3B human liver cell lines, and transcriptional regulation was found to be different in the 3 cell lines. The D LTR subtype was found to have stronger promoter activity than all other types in 4 different human cell lines (HepG2, Hep3B, U251, and 293). Using computational approaches, the D type was shown to contain 4 transcription factor-binding sites distinct from those in the U3 regions of the other subtypes. Therefore, deletion mutants were constructed and examined by a transient transfection luciferase assay. The results of this analysis indicated that the binding site for the Hand1:E47 transcription factor might play a positive role in the transcriptional regulation of PERV LTR subtype D in human liver cell lines.
허재원,하홍석,김윤지,이자랑,김대수,조병욱,김희수 한국유전학회 2007 Genes & Genomics Vol.29 No.2
sent a potential infectious risk in pig-to-human transplantations. Solitary long terminal repeat (LTR) elements from the PERVs are investigated by PCR amplification, methylation analyses, and promoter asays. Among 6 diferent hybrid individuals (KYP1-6) of KDP (Korean domestic pig)× Yorkshire, a haploid genome of KYP1 and KYP5, while the LTRs from PERV-A5, -A7, and -A8 loci were detected in the diploid genome of all hybrid pigs. Methylation analyses of those solitary LTR elements using genomic DNAs of various tisues from pigs indicated that the solitary LTR element from the PERV-X9 locus was hypomethylated, whereas the solitary LTR elements froloci were hypermethylated in most tisues examined. The solitary LTR element of the PERV-X9-KYP1 clone that had recently integrated into the haploid genome showed les promoter activity than the older PERV-A5-KYP1, PERV-A7-KYP1, PERV-A8-KYP1 LTRs detected in diploid genome of pigs. Our data suggest that the LTR elements having high al activity in various tissues of pigs.
허재원,하홍석,김대수,조병욱,김희수 한국유전학회 2007 Genes & Genomics Vol.29 No.3
The characteristic phenotype of partial trisomy 14 includes growth and developmental Porcine endogenous retroviruses (PERVs) in the pig genome represent potential infectious risk factors in pig-to-human transplantation. Solitary long terminal repeat (LTR) elements of the PERV specificaly afect the replication properties of single viruses and adjacent genes through their transcription factors. The promoter activity of solitary LTR elements belonging to the PERV-A and -B families in Korean wild pig (KWP) using a luciferase assay were examined. Five types of LTR structure (PERV-A5-KWP, PERV-A6-KWP1, PERV-A6-KWP2, PERV-A7-KWP, PERV-A8-KWP) showed different promoter activity in human HCT116 and COS7 cels. PERV-A6-KWP locus harbors the diferent copy number (seven or eight) of 39 bp repeats located in U3 region and showed diferent promoter activity. Our data sugests that copy numbers of 39 bp repeats and specific insertion and deletion (INDEL) sequences in the U3 region of a solitary LTR element could regulate the diferent transcription activity in pig genome.
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 Molecular Characterization of PERV Gamma1 Long Terminal Repeats
허재원,김대수,하홍석,안궁,장규태,조병욱,김희수 한국분자세포생물학회 2009 Molecules and cells Vol.27 No.1
Porcine endogenous retroviruses (PERVs) gamma1 in the pig genome have the potential to act as harmful factors in xenotransplantation (pig-to-human). Long terminal repeats (LTRs) are known to be strong promoter elements that could control the transcription activity of PERV elements and the adjacent functional genes. To investigate the transcribed PERV gamma1 LTR elements in pig tissues, bioinformatic and experimental approaches were conducted. Using RT-PCR amplification and sequencing approaches, 69 different transcribed LTR elements were identified. And 69 LTR elements could be divided into six groups (15 subgroups) by internal variation including tandem repeated sequences, insertion and deletion (INDEL). Remarkably, all internal variations were indentified in U3 region of LTR elements. Taken together, the identification and characterization of various PERV LTR transcripts allow us to extend our knowledge of PERV and its transcriptional study.