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Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements
Gim, Jeong-An,Ha, Hong-Seok,Ahn, Kung,Kim, Dae-Soo,Kim, Heui-Soo Korea Genome Organization 2014 Genomics & informatics Vol.12 No.4
MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.
Gim, Jeong-An,Hong, Chang Pyo,Kim, Dae-Soo,Moon, Jae-Woo,Choi, Yuri,Eo, Jungwoo,Kwon, Yun-Jeong,Lee, Ja-Rang,Jung, Yi-Deun,Bae, Jin-Han,Choi, Bong-Hwan,Ko, Junsu,Song, Sanghoon,Ahn, Kung,Ha, Hong-Seok Korean Society for Molecular and Cellular Biology 2015 Molecules and cells Vol.38 No.3
Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethy-lated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.
Quantitative Expression Analysis of Functional Genes in Four Dog Breeds
Jeong-An Gim(김정안),Sang-Hoon Kim(김상훈),Hee-Eun Lee(이희은),Hoim Jeong(정호임),Gyu-Hwi Nam(남규휘),Min Kyu Kim(김민규),Jae-Won Huh(허재원),Bong-Hwan Choi(최봉환),Heui-Soo Kim(김희수) 한국생명과학회 2015 생명과학회지 Vol.25 No.8
가축화된 동물종 중 하나인 개는, 다양한 목적을 위해 인간에 의하여 선택적으로 육종되었다. 개는 많은 품종을 갖고 있고, 특정한 행동과 형태를 갖도록 인공적으로 선택되어 왔다. 개들은 그들의 삶을 안내, 구조 혹은 탐지등의 특수 목적에 대하여 인간에게 헌신하고 있다. 특수 목적견에게 요구되는 좋은 품성, 이를테면 온순함, 강건성, 그리고 인내심과 같은 특성은 그들의 특수 임무를 수행하는 데 필요하다. 많은 연구들이 우수한 특수 목적견의 선정을 위한 유전적 마커를 찾는 데 집중되었다. 본 연구에서는, 뇌에서 발현함으로써 기능하는 것으로 알려진 총 8개의 유전자(ABAT; 4-Aminobutyrate Aminotransferase, PLCB1; Phospholipase C, Beta 1, SLC10A4; Solute Carrier Family 10, Member 4, WNT1; Wingless-Type MMTV Integration Site Family, Member 1, BARX2;BarH-Like Homeobox 2, NEUROD6; Neuronal Differentiation 6, SEPT9; Septin 9 그리고 TBR1; T-Box, Brain, 1)들의 정량적인 발현 양상을 개의 네 품종의 뇌 조직에서 확인하였다. 특히, BARX2, SEPT9, SLC10A4, TBR1 그리고 WNT1 유전자들은 비글과 진돗개에서 많이 발현되는데 반하여, 삽살이와 세퍼드에서는 반대되는 발현 양상을 보여 주었다. 본 연구의 유전자들에 대한 Gene ontology (GO) 결정을 위하여 DAVID (Database for annotation, visualization and integrated discovery) 분석이 수행되었고, 이러한 유전자들이 뇌 발생과 개체의 지능에 중요한 기능을 제공할 것이라고 예상하였다. 결론적으로, 이러한 결과들을 통하여, 뇌에서의 기능과 관련된 인자들과 관련된 바이오마커를 발굴하는 데 중요한 단서를 제공해 줌과 동시에, 우수한 특수 목적견을 선발하는 데 도움을 줄 것이라 기대한다. One of the domesticated species; the dog has been selectively bred for various aims by human. The dog has many breeds, which are artificially selected for specific behaviors and morphologies. Dogs contribute their life to human as working dogs for guide, rescue, detection or etc. Working dogs requires good personality, such as gentleness, robustness and patience for performing their special duty. Many studies have concentrated on finding genetic marker for selecting the high-quality working dog. In this study, we confirmed quantitative expression patterns of eight genes (ABAT; 4-Aminobutyrate Aminotransferase, PLCB1; Phospholipase C, Beta 1, SLC10A4; Solute Carrier Family 10, Member 4, WNT1; Wingless-Type MMTV Integration Site Family, Member 1, BARX2; BarH-Like Homeobox 2, NEUROD6; Neuronal Differentiation 6, SEPT9; Septin 9 and TBR1; T-Box, Brain, 1) among brains tissues from four dog breeds (Beagle, Sapsaree, Shepherd and Jindo), because these genes were expressed and have functions in brain mostly. Specially, BARX2, SEPT9, SLC10A4, TBR1 and WNT1 genes were highly expressed in Beagle and Jindo, and Sapsaree and German Shepherd were vice versa. The biological significance of total genes was estimated by database for annotation, visualization and integrated discovery (DAVID) to determine a different gene ontology (GO) class. In these analyses, we suppose to these eight genes could provide influential information for brain development, and intelligence of organisms. Taken together, these results could provide clues to discover biomarker related to functional traits in brain, and beneficial for selecting superior working dogs.
Genetic diversity and population structure of three dog breeds through microsatellite loci analysis
Hoim Jeong(정호임),Bong-Hwan Choi,Jungwoo Eo,Yun-Jeong Kwon,Hee-Eun Lee,Yuri Choi,Jeong-An Gim,Tae-Hun Kim,Hwan-Hoo Seong,Dong-Hoon Lee,Ji-Hong Ha,Kook-Il Han,Heui-Soo Kim 한국실험동물학회 2014 한국실험동물학회 학술발표대회 논문집 Vol.2014 No.8
Identification and Expression of Equine MER-Derived miRNAs
Gim, Jeong-An,Kim, Heui-Soo Korean Society for Molecular and Cellular Biology 2017 Molecules and cells Vol.40 No.4
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns. The MER5A1, MER53, and MER91C sequences obtained from RepeatMasker were matched with the eca-miR-544b, eca-miR-1302, and eca-miR-652 precursor sequences derived from Ensembl transcript database, respectively. Each precursor form was anticipated to yield two mature forms, and we confirmed miRNA expression in six different tissues (cerebrum, cerebellum, lung, spleen, adrenal gland, and duodenum) of one thoroughbred horse. MER5A1-derived miRNAs generally showed significantly higher expression in the lung than in other tissues. MER91C-derived miRNA-5p also showed significantly higher expression in the duodenum than in other tissues (cerebellum, lung, spleen, and adrenal gland). The MER117-overlapped expressed sequence tag generated polycistronic miRNAs, which showed higher expression in the duodenum than other tissues. These data indicate that horse MER transposons encode miRNAs that are expressed in several tissues and are thought to have biological functions.
Drosophila Med6 is required for proliferation and metabolism associated with larval metamorphosis
Gim, Byung Soo,Park, Jin Mo,Yoon, Jeong Ho,Kang, Chang Won,Kim, Young-Joon 이화여자대학교 세포신호전달연구센터 2001 고사리 세포신호전달 심포지움 Vol. No.3
Mediator of transcriptional regulation is the evolutionary conserved co activator complex that plays the central role in the integration and recruitment of diverse regulatory signals and transcription machinery to certain promoters. In yeast, each Mediator subunit is required for transcriptional regulation of a distinct group of genes. In order to elucidate the functions of metazoan Mediator proteins, we isolated mutants of a conserved Mediator subunit, Drosophila Med6(dMed6). dMed6 null homozygotes failed to pupate and died in the third larval instar. Larval mitotic cells and most imaginal discs showed severe defects in proliferation, but no apparent morphological defect was observed in other larval tissues. Clonal analysis of dMed6 mutant cells revealed that dMed6 is essential for cell viability and proliferation of most adult cell types. Drosophila cDNA microarray, quantitative RT-PCR, and in situ expression analyses of developmentally regulated genes in dMed6 mutants showed that transcriptional activation of a subset of genes involved in cell proliferation and metabolism were most affected. Our results suggest that dMed6 is required in most cells for transcriptional regulation of a subset of genes important for cell proliferation and metabolism.