Kyung-Do Park

Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.

BackgroundThoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes.ResultsWe present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not match any current equine gene model. We also identified 189,973 single nucleotide variations (SNVs) from the sequences aligned against the horse reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases. Using differential expression analysis, we further identified a number of exercise-regulated genes: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle. Six of 28 previously-known exercise-related genes were over-expressed in the muscle after exercise. Among the differentially expressed genes, there were 91 transcription factor-encoding genes, which included 56 functionally unknown transcription factor candidates that are probably associated with an early regulatory exercise mechanism. In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.ConclusionThe first sequencing-based horse transcriptome data, extensive analyses results, deferentially expressed genes before and after exercise, and candidate genes that are related to the exercise are provided in this study.

Genome-wide analysis of DNA methylation patterns in horse

BackgroundDNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known.ResultsWe report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.ConclusionsWe provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.

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

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.

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

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 hypomethylated 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.

Identification of Polymorphisms in CAST Gene Associated with Economic Traits in Hanwoo (Bos taurus coreanae)

A number of studies have shown that the calpain system is important in normal skeletal muscle growth. An increased rate of skeletal muscle growth can result from a decreased rate of muscle protein degradation, and this is associated with a decrease in activity of the calpain system, due principally to a large increase in calpastatin (CAST) activity. The CAST gene, mapped to BTA 7, is considered a candidate gene for beef tenderness and muscle growth. The present study used comparative sequencing of five novel polymorphisms located within exon 20 and 22 of the bovine CAST gene in Hanwoo: exon20- 109737G/A, 109749T/C, 109823T/C, exon22- 116151G/A, intron- 109926G/A. The association of the CAST SNPs with economic traits was studied. The 109926G/A showed a significant effect only on the longissimus muscle area (LMA, p

Antibacterial Activity of Novel Naphthoquiones Derivatives

Abstractl,4-naphthoquinone moiety is Known to confer numerous molecules with distinct-hiological activities including anti -mycobacterial, anticancer and anti-inflammatory activities. Vitamin K2, doxorubicin and mitomycin are among the few examples of this class of chemicals used in the treatment of bleeding, lymphoma and carcinoma respectively. Although the exact action mechanism of these molecules is still under investigation, proposed mechanisms include their interact ion with DNA inhibition of topoisomerase II, and production of ROS, contributing individually or in combination with DNA damage and cell death . In the present study, 6 naphthoquinones were synthesized and assayed for their antimicrobial activity againstStaphylococcus aureus by disc diffusion assay and spectrophotometric analys is. DNA topoisomerase II activity was also measured to investigate the degreee of conformation change of a test plasmid DNA affected by the naphthoquinone deriva tives.

Copy number deletion has little impact on gene expression levels in racehorses.

Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

Identification of ORF sequences and exercise-induced expression change in thoroughbred horse OXCT1 gene.

In the mitochondrial matrix, the OXCT1 gene catalyzes the reversible transfer of coenzyme A from succinyl-CoA to acetoacetate in a reaction related to energy production from ketone bodies. Here, horse OXCT1 gene containing coenzyme A transferase domain was identified in the transcriptome analysis of cDNAs derived from skeletal muscles. Horse OXCT1 gene consisted of 1761 [corrected] nucleotide sequences with an open reading frame of 1560 nucleotides encoding a protein of 520 putative amino acid residues.The number of non-synonymous substitutions was lower than the number of synonymous substitutions in the OXCT1 genes of other species, indicating that purifying selection occurred in the OXCT1 genes during evolutionary radiation. Quantitative real-time RT-RCR analysis showed a dominant expression pattern of horse OXCT1 gene in the cerebrum, heart, and skeletal muscle. Different expression levels of horse OXCT1 transcripts between before- and after-exercise samples were also measured in the skeletal muscles of six horses. These data could be of great use for further investigation of the relationship between energy products and horse OXCT1 gene.

Effects of Change of Body Weight on Racing Time in Thoroughbred Racehorses

본 연구는 한국마사회로부터 수집한 8,197두의 경주기록 총 155,656개를 이용하여 더러브렛 경주마의 체중변화가 주파기록에 미치는 효과를 구명하기 위하여 수행되었다. 국내 더러브렛 경주마의 평균 체중은 449 kg 이었으며, 거세말, 수말과 암말의 평균 체중은 각각 460 kg, 454 kg과 441 kg으로 수말의 체중이 가장 높게 나타났다. 암말의 경우 체중의 감소는 3월, 4월과 5월사이에 가장 크게 나타나며, 수말과 거세마의 경우 5월, 6월과 7월에 체중의 감소가 가장 크게 나타났다. 전반적으로 경주마의 체중은 봄과 여름에 감소하며, 가을과 겨울에 증가하는 현상을 나타내었다. 주파기록에 대한 유전력과 반복력은 각각 0.237과 0.525였으며, 체중에 대한 유전력은 0.612로 추정되었다. 직전 경주 대비 체중의 변화가 ±10 kg 이상일 때 주파기록은 현저히 증가하였으며, 직전 경주 대비 체중의 변화가 ±20 kg인 경우는 ±5 kg인 경우와 비교했을 때 주파기록의 차이가 0.3초 정도 증가하였다. 체중의 변화가 체중에 비례하여 ±0.5% 정도 변화하였을 때 주파기록이 가장 우수하였으며, 체중의 변화가 체중 대비 ±2.5% 이상이 되면 경주능력은 현저히 감소하였다.(

Estimation of Genetic Parameters for Economic Traits of Hanwoo Cows Using Ultrasound

This experiment was conducted to estimate the genetic parameters and breeding values of the economic traits measured from the cows (aged 15 months or older) using ultrasound and to use them as the information for the selection of stock animals at the farm level. The means and standard deviations of longissimus muscle area, backfat thickness and marbling score were 54.11 cm 2 ± 9.06, 3.57 mm ± 2.45 and 2.65 ± 2.88, respectively. While the linear regression coefficients of longissimus muscle area, backfat thickness and marbling score for age (in months) were all positive (0.3532, 0.0868 and 0.0833), the quadratic regression coefficients of them for age (in months) were all negative ( 0.0023, 0.0005 and 0.0006), and as the body condition score increased longissimus muscle area, backfat thickness and marbling score increased collectively. The heritability estimates for the longissimus muscle area, backfat thickness and marbling score were 0.39, 0.48 and 0.13, respectively and the estimated annual genetic gains for the longissimus muscle area, backfat thickness and marbling score were 0.00334 cm 2 , 0.0073 mm and 0.0043