• Asian-Australasian Journal of Animal Sciences
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• 제27권10호
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• pp.1493-1498
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• 2014

Epigenetic factors, such as DNA methylation status, may regulate adipogenesis and lipogenesis, thus affecting intramuscular fat (IMF) deposition in longissimus dorsi muscle (LM) of beef cattle. In Korean cattle steers, the LM consists mainly of muscle tissue. However, the LM tissue also contains IMF. We compared the gene expression levels between the IMF and muscle portions of the LM after tissue separation. Real-time polymerase chain reaction analysis showed that the mRNA levels of both adipogenic peroxisome proliferator-activated receptor gamma isoform 1 (PPARG1) and lipogenic fatty acid binding protein 4 (FABP4) were higher (p<0.01) in the IMF than in the muscle portion of the LM. We determined DNA methylation levels of regulatory regions of the PPARG1 and FABP4 genes by pyrosequencing of genomic DNA. DNA methylation levels of two of three CpG sites in the PPARG1 gene promoter region were lower (p<0.05) in the IMF than in the muscle portion of the LM. DNA methylation levels of all five CpG sites from the FABP4 gene promoter region were also lower (p<0.001) in the IMF than in the muscle portion. Thus, mRNA levels of both PPARG1 and FABP4 genes were inversely correlated with DNA methylation levels in regulatory regions of CpG sites of the corresponding gene. Our findings suggest that DNA methylation status regulates tissue-specific expression of adipogenic and lipogenic genes in the IMF and muscle portions of LM tissue in Korean cattle.

• Genomics & Informatics
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• 제9권3호
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• pp.136-137
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• 2011

Methylation of cytosine is a post-synthesis modification that does not affect the primary DNA sequence but greatly influences gene expression level and phenotypes of an organism. As high-throughput sequencing of bisulfite-treated DNA is the most efficient method to identify methylated sites, several tools to map sequencing reads on a reference are available. But tools to visualize and to interpret the methylation level of methylation sites are currently insufficient. Herein, we present a novel tool to visualize the methylation level of CpG sites.

• Genomics & Informatics
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• 제4권1호
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• pp.1-10
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• 2006

Epigenetic alterations are common features of human solid tumors, though global DNA methylation has been difficult to assess. Restriction Landmark Genomic Scanning (RLGS) is one of technology to examine epigenetic alterations at several thousand Notl sites of promoter regions in tumor genome. To assess sequence information for Notl sequences in RLGS gel, we cloned 1,161 unique Notl-linked clones, compromising about 60% of the spots in the soluble region of RLGS profile, and performed BLAT searches on the UCSC genome server, May 2004 Freeze. 1,023 (88%) unique sequences were matched to the CpG islands of human genome showing a large bias of RLGS toward identifying potential genes or CpG islands. The cloned Notl-loci had a high frequency (71%) of occurrence within CpG islands near the 5' ends of known genes rather than within CpG islands near the 3' ends or intragenic regions, making RLGS a potent tool for the identification of gene-associated methylation events. By mixing RLGS gels with all Notl-linked clones, we addressed 151 Notl sequences onto a standard RLGS gel and compared them with previous reports from several types of tumors. We hope our sequence information will be useful to identify novel epigenetic targets in any types of tumor genome.

• 생명과학회지
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• 제33권9호
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• pp.730-735
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• 2023

지난 10년 동안 인공지능의 도움으로 노화를 정량화하기 위한 수많은 연구가 수행되었다. DNA 메틸화 데이터를 사용하여 다양한 모델이 개발되었으며 흔히 후성유전학적 시계라고 불린다. 후성유전학적 나이 가속화는 일반적으로 질병 상태와도 주로 연관이 있어 보인다. 조현병은 가속 노화 가설과 관련있는 정신질병으로 심각한 정신적, 신체적 스트레스를 동반한다. 다른 심리 질환과 비교했을 때 이 질병은 젊은 사람들에서 높은 사망률과 질병률을 유발한다. 과거 연구에서는 이 질병이 가속 노화 가설과 연관있다고 알려져 있었다. 이번 연구에서는 조현병 환자의 후성유전학적 나이 가속도 변화를 통해 질병에 대한 후성유전학적 통찰을 얻고자 하였다. 후성유전학적 나이 가속화를 측정하기 위해 두 가지 다른 DNA 메틸화 시계 모델을 사용했으며 이는 범조직 모델인 Horvath clock과 Epi clock을 사용하였다. 우리는 Horvath clock과 Epi clock이 모두 호환되는 450k 어레이 데이터를 사용하였다. 그 결과, Epi clock을 사용했을 때 환자샘플에서 후성유전학적 나이 가속화가 더 느리다는 것을 발견했다. Epi clock이 질병으로 인한 DNA 메틸화 변화를 잘 감지해낼 수 있음을 알아내었다. 또한 Epi clock에서 대조군과 환자군에서 차등적으로 메틸화된 CpG 부위를 분석하고 경로 농축 분석을 수행한 결과, 대부분의 CpG가 신경 세포 과정에 관여한다는 사실을 발견했다.

• Genomics & Informatics
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• 제15권4호
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• pp.170-177
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• 2017

HOTAIR is an lncRNA that has been known to have an oncogenic role in different cancers. There is limited knowledge of genetic and epigenetic elements and their interactions for the gene encoding HOTAIR. Therefore, understanding the molecular mechanism and its regulation remains to be challenging. We used different in silico analyses to find genetic and epigenetic elements of HOTAIR gene to gain insight into its regulation. We reported different regulatory elements including canonical promoters, transcription start sites, CpGIs as well as epigenetic marks that are potentially involved in the regulation of HOTAIR gene expression. We identified repeat sequences and single nucleotide polymorphisms that are located within or next to the CpGIs of HOTAIR. Our analyses may help to find potential interactions between genetic and epigenetic elements of HOTAIR gene in the human tissues and show opportunities and limitations for researches on HOTAIR gene in future studies.

• BMB Reports
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• 제52권10호
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• pp.577-588
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• 2019

DNA methylation at CpG sites is an essential epigenetic mark that regulates gene expression during mammalian development and diseases. Methylome refers to the entire set of methylation modifications present in the whole genome. Over the last several years, an increasing number of reports on brain DNA methylome reported the association between aberrant methylation and the abnormalities in the expression of critical genes known to have critical roles during aging and neurodegenerative diseases. Consequently, the role of methylation in understanding neurodegenerative diseases has been under focus. This review outlines the current knowledge of the human brain DNA methylomes during aging and neurodegenerative diseases. We describe the differentially methylated genes from fetal stage to old age and their biological functions. Additionally, we summarize the key aspects and methylated genes identified from brain methylome studies on neurodegenerative diseases. The brain methylome studies could provide a basis for studying the functional aspects of neurodegenerative diseases.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2001년도 춘계학술발표대회
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• pp.15-15
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• 2001

We recently demonstrated that satellite regions exhibit an aberrant DNA methylation in cloned bovine embryos. Here, we examined, using bisulfite -sequencing technology, whether the inefficient demethylation of cloned donor genomes could be rescued by the presence of oocytic nuclei. Both AciI digestion and sequencing analyses showed that satellite sequence was demethylated more efficiently in cloned tetraploid blastocysts than in diploid clones. When methyl -CpG density (the number of methyl-CpG sites per string) was scored, a significant decrease was observed In tetraploids (P<0.001). These results suggest that unknown mechanisms provided by oocytic nuclei could assist the demethylation of satellite sequences in tetraploid clones.

• Asian-Australasian Journal of Animal Sciences
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• 제32권2호
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• pp.170-175
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• 2019

Objective: Uncoupling protein 3 gene (UCP3) is a candidate gene associated with the meat quality of pigs. The aim of this study was to explore the regulation mechanism of UCP3 expression and provide a theoretical basis for the research of the function of porcine UCP3 gene in meat quality. Methods: Bisulfite sequencing polymerase chain reaction (PCR) and quantitative real-time PCR (Q-PCR) were used to analyze the methylation of UCP3 5′-flanking region and UCP3 mRNA expression in the adipose tissue or skeletal muscle of three pig breeds at different ages (1, 90, 210-day-old Putian Black pig; 90-day-old Duroc; and 90-day-old Dupu). Results: Results showed that two cytosine-guanine dinucleotide (CpG) islands are present in the promoter region of porcine UCP3 gene. The second CpG island located in the core promoter region contained 9 CpG sites. The methylation level of CpG island 2 was lower in the adipose tissue and skeletal muscle of 90-day-old Putian Black pigs compared with 1-day-old and 210-day-old Putian Black pigs, and the difference also existed in the skeletal muscle among the three 90-day-old pig breeds. Furthermore, the obvious changing difference of UCP3 mRNA expression was observed in the skeletal muscle of different groups. However, the difference of methylation status and expression level of UCP3 gene was not significant in the adipose tissue. Conclusion: Our data indicate that UCP3 mRNA expression level was associated with the methylation status of UCP3 promoter in the skeletal muscle of pigs.

• Journal of Species Research
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• 제10권2호
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• pp.154-158
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• 2021

An endemic endangered species, Aster altaicus var. uchiyamae (Danyang aster) B2015-0044, is cultivated at the Shingu Botanical Garden, which serves as the ex situ conservation institution for this species. In this work, we sequenced the chloroplast genome of A. altaicus var. uchiyamae B2015-0044. We found that the chloroplast (cp) genome of B2015-0044 was 152,457 base pairs(bps) in size: 84,247 bps of large single copy regions(LSC), 25,007 bps of inverted repeats(IRs), and 18,196 bps of small single copy regions. The B2015-0044 cp genome contains 79 protein-coding genes (PCGs), 4 RNA genes, 29 tRNA genes, and 3 pseudogenes. These results were identical to a previously reported cp genome (Park et al., 2017), except for two sites in introns and three in intergenic spacer (IGS) regions. For the intronic differences, we found that clpP.i1 had a 1-bp small simple repeat (SSR) (T) and petD.i had a 3-bp SSR (ATT). We found 1-bp SSRs in the IGSs of trnT_ggu~psbD and psbZ~trnG_gcc, C and A, respectively. The IGS of(ndhF)~rpl32 had a SNP. Based on our results, the cp genome of the A. altaicus var. uchiyamae can be classified into two genotypes, [C]¹-[A]¹²-[T]¹²-[ATT]⁴-C and [C]²-[A]¹¹-[T]¹¹-[ATT]²-A.

• Molecules and Cells
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• 제40권5호
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• pp.346-354
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• 2017

Long interspersed nuclear element-1 (LINE-1) is a retrotransposon that contains a CpG island in its 5'-untranslated region. The CpG island of LINE-1 is often heavily methylated in normal somatic cells, which is associated with poor prognosis in various cancers. DNA methylation can differ between formalin-fixed paraffin-embedded (FFPE) and frozen tissues. Therefore, this study aimed to compare the LINE-1 methylation status between the two tissue-storage conditions in gastric cancer (GC) clinical samples and to evaluate whether LINE-1 can be used as an independent prognostic marker for each tissue-storage type. We analyzed four CpG sites of LINE-1 and examined the methylation levels at these sites in 25 FFPE and 41 frozen GC tissues by quantitative bisulfite pyrosequencing. The LINE-1 methylation status was significantly different between the FFPE and frozen GC tissues (p < 0.001). We further analyzed the clinicopathological features in the two groups separately. In the frozen GC tissues, LINE-1 was significantly hypomethylated in GC tissues compared to their corresponding normal gastric mucosa tissues (p < 0.001), and its methylation status was associated with gender, differentiation state, and lymphatic and venous invasion of GC. In the FFPE GC tissues, the methylation levels of LINE-1 differed according to tumor location and venous invasion of GC. In conclusion, LINE-1 can be used as a useful methylation marker for venous invasion in both FFPE and frozen tumor tissues of GC.