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.

Identification and expression analysis of human endogenous retrovirus Y (HERV-Y) in various human tissues

Gim, Jeong-An,Han, Kyudong,Kim, Heui-Soo Springer-Verlag 2015 Archives of virology Vol.160 No.9

Genome-Wide Analysis of DNA Methylation before- and after Exercise in the Thoroughbred Horse with MeDIP-Seq

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.

Draft genome of Semisulcospira libertina, a species of freshwater snail

Gim, Jeong-An,Baek, Kyung-Wan,Hah, Young-Sool,Choo, Ho Jin,Kim, Ji-Seok,Yoo, Jun-Il Korea Genome Organization 2021 Genomics & informatics Vol.19 No.3

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S. libertina was estimated to be 3.04 Gb. Using RepeatMasker, a total of 53.68% of repeats were identified in the genome assembly. Genome data of S. libertina reported in this study will be useful for identification and conservation of S. libertina in East Asia.

Identification and Expression Analyses of Equine Endogenous Retroviruses in Horses

Gim, Jeong-An,Kim, Heui-Soo Korean Society for Molecular and Cellular Biology 2017 Molecules and cells Vol.40 No.10

Endogenous retroviruses (ERVs) have been integrated into vertebrate genomes and have momentously affected host organisms. Horses (Equus caballus) have been domesticated and selected for elite racing ability over centuries. ERVs played an important role in the evolutionary diversification of the horse genome. In the present study, we identified six equine ERV families (EqERVs-E1, I1, M2, P1, S1, and Y4), their full-length viral open reading frames (ORFs), and elucidated their phylogenetic relationships. The divergence time of EqERV families assuming an evolutionary rate of 0.2%/Myr indicated that EqERV-S3 (75.4 million years ago; mya) on chromosome 10 is an old EqERV family and EqERV-P5 (1.2 Mya) on chromosome 12 is a young member. During the evolutionary diversification of horses, the EqERV-I family diverged 1.7 Mya to 38.7 Mya. Reverse transcription quantitative real-time PCR (RT-qPCR) amplification of EqERV pol genes showed greater expression in the cerebellum of the Jeju horse than the Thoroughbred horse. These results could contribute further dynamic studies for horse genome in relation to EqERV gene function.

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.

Demographic and Genome Wide Association Analyses According to Muscle Mass Using Data of the Korean Genome and Epidemiology Study

Gim Jeong-An,Lee Sangyeob,Kim Seung Chan,Baek Kyung-Wan,Yoo Jun-Il 대한의학회 2022 Journal of Korean medical science Vol.37 No.50

Background: Sarcopenia is commonly found in the elderly due to a decline in muscle mass. Many researchers have performed genome-wide association studies (GWAS) to find genetic risk factors of sarcopenia. Although many studies have discovered sarcopenia associated single nucleotide polymorphisms (SNPs), most of them are studies targeting Caucasians. The purpose of this study was to evaluate genetic correlation according to muscle mass in middle aged Koreans using data of the Korean Genome and Epidemiology Study (KOGES), a large population-based genomic cohort study. Methods: Baseline participants were 10,030 subjects aged 40 to 69 years who were from Ansan or Anseong in Gyeonggi-do, South Korea. Among them, 9,351 subjects with laboratory data available were included in this study. To identify sarcopenia associated variants, those in the top 30% and bottom 30% of muscle mass index (MMI) were compared. A total of 7,452 people with an MMI of 30-70% were excluded. A total of 1,004 people were also excluded due to missing data. Finally, 895 people were selected for this study. The Korea Biobank Array generated 500,568 SNPs for this dataset. Results: When subjects were divided into top 30% and bottom 30% of MMI, the top 30% had 169 men and 308 women and the bottom 30% had 220 men and 198 women. In men, age, body mass index (BMI), waist and hip were significantly (P < 0.005) different between top 30% and bottom 30% MMI groups. In women, age, BMI, waist, hip, and hypertension history were significantly different between the two MMI groups. There were 13 significant SNPs in men and 14 significant SNPs in women. Genes associated with variants in men based on the single-nucleotide polymorphism database (dbSNP) were LRP1B containing rs11679458 and RGS6 containing rs11848300. A gene associated with variants in women was Pi4K2A, which contained rs1189312 as a variant. In addition, rs11189312 was associated with expression quantitative trait loci (eQTL) of ZFYVE27 in skeletal muscles and other SNPs of ZFYVE27 (rs10882883, rs17108378, rs35077384) known to be associated with spastic paraplegia. The eQTL analysis revealed that rs11189312 was a variant associated with SNPs of ZFYVE27. Conclusions: In the demographic study, significant results were found in BMI, waist, hip, history of hyperlipidemia, and sedentary life status in male group, and significant results were found in BMI, waist, hip, and hypertension history in female group. Variant rs11189312 was found to be a novel variant affecting ZFYVE27 expressed in skeletal muscles, suggesting that rs11189312 might be related to sarcopenia as a novel discovery of this study. Further study is needed to determine the association between sarcopenia and ZFYVE27 known to be associated with spastic paraplegia.

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.

NGS 기법을 활용한 전장게놈에서의 경제형질 관련 유전자 마커 발굴

김정안(Jeong-An Gim),김희수(Heui-Soo Kim) 한국생명과학회 2014 생명과학회지 Vol.24 No.11

가축의 고 성장률, 강건성, 질병 저항성과 같은 경제적 형질을 발굴하는 것은 매우 중요한 과제이다. 이에 경제적 형질을 발굴하기 위한 방법으로 전통적으로 RFLP, AFLP와 같은 방법이 대두되었으며, 최근 NGS 기법이 발달함에 따라 이러한 경제적 형질을 전장게놈의 수준에서 발굴하려는 노력이 계속되고 있다. 하지만, NGS 기법의 경우 상대적으로 많은 연구 비용이 필요한 실정이다. 이를 극복하기 위한 노력으로써 RNA-seq, RAD-Seq, RRL, MSG, GBS 등과 같은 기법이 활용되고 있다. 본 논문에서는 NGS 기법을 기반으로 한 최근 연구 동향을 확인하고자 하며, 특히 최소의 연구 비용으로 최대의 효과를 낼 수 있는 연구 방법을 소개하는 데 초점을 맞추었다. 또한 이러한 연구 방법이 우수한 경제형질을 가진 가축을 선정하는 데 어떻게 적용될 수 있는지에 대해 토의하였다. Developing economic traits with a high growth rate, robustness, and disease resistance in livestock is an important challenge. RFLP and AFLP are the classical methods used to develop economic traits. Whole-genome-based economic traits have recently been detected with the advent of next-generation sequencing (NGS) technologies. However, NGS technologies are rather costly for use in studies, and RNA-seq, RAD-Seq, RRL, MSG, and GBS have been used to overcome the issue of high costs. In this study, recent NGS-based studies were reviewed, particularly those that focused on minimum costs and maximum effects. Then, we presented further prospects on how to apply for selection of high economic-trait livestock.

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