• Genes and Genomics
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• 제40권11호
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• pp.1157-1167
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• 2018

Sulfolobus species can grow on a variety of organic compounds as carbon and energy sources. These species degrade glucose to pyruvate by the modified branched Entner-Doudoroff pathway. We attempted to determine the differentially expressed genes (DEGs) under sugar-limited and sugar-rich conditions. RNA sequencing (RNA-seq) was used to quantify the expression of the genes and identify those DEGs between the S. acidocaldarius cells grown under sugar-rich (YT with glucose) and sugar-limited (YT only) conditions. The functions and pathways of the DEGs were examined using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Quantitative real-time PCR (qRT-PCR) was performed to validate the DEGs. Transcriptome analysis of the DSM 639 strain grown on sugar-limited and sugar-rich media revealed that 853 genes were differentially expressed, among which 481 were upregulated and 372 were downregulated under the glucose-supplemented condition. In particular, 70 genes showed significant changes in expression levels of ${\geq}$ twofold. GO and KEGG enrichment analyses revealed that the genes encoding components of central carbon metabolism, the respiratory chain, and protein and amino acid biosynthetic machinery were upregulated under the glucose condition. RNA-seq and qRT-PCR analyses indicated that the sulfur assimilation genes (Saci_2197-2204) including phosphoadenosine phosphosulfate reductase and sulfite reductase were significantly upregulated in the presence of glucose. The present study revealed metabolic networks in S. acidocaldarius that are induced in a glucose-dependent manner, improving our understanding of biomass production under sugar-rich conditions.

• Journal of Microbiology and Biotechnology
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• 제34권2호
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• pp.270-279
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• 2024

Macrophages are versatile immune cells that play crucial roles in tissue repair, immune defense, and the regulation of immune responses. In the context of skeletal muscle, they are vital for maintaining muscle homeostasis but macrophage-induced chronic inflammation can lead to muscle dysfunction, resulting in skeletal muscle atrophy characterized by reduced muscle mass and impaired insulin regulation and glucose uptake. Although the involvement of macrophage-secreted factors in inflammation-induced muscle atrophy is well-established, the precise intracellular signaling pathways and secretion factors affecting skeletal muscle homeostasis require further investigation. This study aimed to explore the regulation of macrophage-secreted factors and their impact on muscle atrophy and glucose metabolism. By employing RNA sequencing (RNA-seq) and proteome array, we uncovered that factors secreted by lipopolysaccharide (LPS)-stimulated macrophages upregulated markers of muscle atrophy and pro-inflammatory cytokines, while concurrently reducing glucose uptake in muscle cells. The RNA-seq analysis identified alterations in gene expression patterns associated with immune system pathways and nutrient metabolism. The utilization of gene ontology (GO) analysis and proteome array with macrophage-conditioned media revealed the involvement of macrophage-secreted cytokines and chemokines associated with muscle atrophy. These findings offer valuable insights into the regulatory mechanisms of macrophage-secreted factors and their contributions to muscle-related diseases.

• Molecules and Cells
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• 제45권9호
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• pp.622-630
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• 2022

Colorectal cancer (CRC) has a high mortality rate among cancers worldwide. To reduce this mortality rate, chemotherapy (5-fluorouracil, oxaliplatin, and irinotecan) or targeted therapy (bevacizumab, cetuximab, and panitumumab) has been used to treat CRC. However, due to various side effects and poor responses to CRC treatment, novel therapeutic targets for drug development are needed. In this study, we identified the overexpression of EHMT1 in CRC using RNA sequencing (RNA-seq) data derived from TCGA, and we observed that knocking down EHMT1 expression suppressed cell growth by inducing cell apoptosis in CRC cell lines. In Gene Ontology (GO) term analysis using RNA-seq data, apoptosis-related terms were enriched after EHMT1 knockdown. Moreover, we identified the CHOP gene as a direct target of EHMT1 using a ChIP (chromatin immunoprecipitation) assay with an anti-histone 3 lysine 9 dimethylation (H3K9me2) antibody. Finally, after cotransfection with siEHMT1 and siCHOP, we again confirmed that CHOP-mediated cell apoptosis was induced by EHMT1 knockdown. Our findings reveal that EHMT1 plays a key role in regulating CRC cell apoptosis, suggesting that EHMT1 may be a therapeutic target for the development of cancer inhibitors.

• 생명과학회지
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• 제24권11호
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• pp.1258-1267
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• 2014

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.

• 한국가금학회지
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• 제41권4호
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• pp.287-296
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• 2014

조류의 난포 성장은 호르몬의 작용에 따라 크기가 달라져 각각의 단계를 이루며 성장하게 된다. 난의 성숙에 관련된 유전자는 난 단백질 생산과 산란률에 밀접한 관련이 있으며, 이를 유전자 발현 측면에서 심도 있는 고찰이 필요가 있다. 본 연구는 NGS를 이용한 RNA-seq 데이터를 이용하여 유전자의 발현량과 유전자 상호 구조에 대한 분석을 실시하여 난의 발달 과정에 필요한 유전자군을 조사하였다. 본 실험에 사용된 개체는 한국 재래계 흑색계통이 사용되었고, 비교조직은 미성숙란과 성숙란의 RNA를 추출하여 유전자의 발현 양상을 살펴봄으로 난의 성숙에 필요한 유전자의 발현 양상을 보고자 하였다. 실험을 위해 Total RNA를 추출하였고, HiSeq 2000 platform을 사용하여 염기서열을 분석하고, Tuxedo Protocol과 DAVID 프로그램을 통해 유전자의 기능과 상호간의 연관관계를 예측하였다. 탐색된 유전자군은 미성숙란과 성숙란 간에 많은 차이를 보이고 있는 유전자군을 탐색한 결과, 315개의 발현이 다르게 나타나는 것으로 보이고 있으며, GO 분석을 통하여 기능면에서 미성숙란과 성숙란에서 확연히 구분되는 유전자 발현 양상을 확인할 수 있었다. 이들 결과를 통하여 향후 난성숙 과정을 이해하고, 계란 품질 향상을 위한 마커 개발을 기여할 수 있을 것으로 사료된다.

• Molecules and Cells
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• 제37권1호
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• pp.81-87
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• 2014

Chronic pressure-overload cardiac hypertrophy is associated with an increased risk of morbidity/mortality, largely due to maladaptive remodeling and dilatation that progresses to dilated cardiomyopathy. Alternative splicing is an important biological mechanism that generates proteomic complexity and diversity. The recent development of next-generation RNA sequencing has improved our understanding of the qualitative signatures associated with alternative splicing in various biological conditions. However, the role of alternative splicing in cardiac hypertrophy is yet unknown. The present study employed RNA-Seq and a bioinformatic approach to detect the RNA splicing regulatory elements involved in alternative splicing during pressure-overload cardiac hypertrophy. We found GC-rich exonic motifs that regulate intron retention in 5' UTRs and AT-rich exonic motifs that are involved in exclusion of the AT-rich elements that cause mRNA instability in 3' UTRs. We also identified motifs in the intronic regions involved in exon exclusion and inclusion, which predicted splicing factors that bind to these motifs. We found, through Western blotting, that the expression levels of three splicing factors, ESRP1, PTB and SF2/ASF, were significantly altered during cardiac hypertrophy. Collectively, the present results suggest that chronic pressure-overload hypertrophy is closely associated with distinct alternative splicing due to altered expression of splicing factors.

• 인터넷정보학회논문지
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• 제20권4호
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• pp.21-27
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• 2019

RNA 시퀀싱 데이터 (RNA-seq)에서 수집된 많은 양의 데이터에 변별력이 확실한 특징 패턴 선택이 유용하며, 차별성 있는 특징을 정의하는 것이 쉽지 않다. 이러한 이유는 빅데이터 자체의 특징으로써, 많은 양의 데이터에 중복이 포함되어 있기 때문이다. 해당이슈 때문에, 컴퓨터를 사용하여 처리하는 분야에서 특징 선택은 랜덤 포레스트, K-Nearest, 및 서포트-벡터-머신 (SVM)과 같은 다양한 머신러닝 기법을 도입하여 해결하려고 노력한다. 해당 분야에서도 SVM-기반 제약을 사용하는 서포트-벡터-머신-재귀-특징-제거(SVM-RFE) 알고리즘은 많은 연구자들에 의해 꾸준히 연구 되어 왔다. 본 논문의 제안 방법은 RNA 시퀀싱 데이터에서 빅-데이터처리를 위해 SVM-RFE에 강화학습의 Q-learning을 접목하여, 중요도가 추가되는 벡터를 세밀하게 추출함으로써, 변별력이 확실한 특징선택 방법을 제안한다. NCBI-GEO와 같은 빅-데이터에서 공개된 일부의 리보솜 단백질 클러스터 데이터에 본 논문에서 제안된 알고리즘을 적용하고, 해당 알고리즘에 의해 나온 결과와 이전 공개된 SVM의 Welch' T를 적용한 알고리즘의 결과를 비교 평가하였다. 해당결과의 비교가 본 논문에서 제안하는 알고리즘이 좀 더 나은 성능을 보여줌을 알 수 있다.

• Asian-Australasian Journal of Animal Sciences
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• 제32권12호
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• pp.1816-1825
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• 2019

Objective: We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal crosses between Korean Native and Landrace pigs. Methods: We carried out sequencing of parental genomes and offspring transcriptomes using next generation sequencing. We subsequently carried out genome scale identification of single nucleotide polymorphisms (SNPs) in two different ways using either individual genome mapping or joint genome mapping of the same breed parents that were used for the reciprocal crosses. Using parent-specific SNPs, allele-specifically expressed genes were analyzed. Results: Because of the low genome coverage (${\sim}4{\times}$) of the sequencing results, most SNPs were non-informative for parental lineage determination of the expressed alleles in the offspring and were thus excluded from our analysis. Consequently, 436 SNPs covering 336 genes were applicable to measure the imbalanced expression of paternal alleles in the offspring. By calculating the read ratios of parental alleles in the offspring, we identified seven genes showing allele-biased expression (p<0.05) including three previously reported and four newly identified genes in this study. Conclusion: The newly identified allele-specifically expressing genes in the neocortex of pigs should contribute to improving our knowledge on genomic imprinting in pigs. To our knowledge, this is the first study of allelic imbalance using high throughput analysis of both parental genomes and offspring transcriptomes of the reciprocal cross in outbred animals. Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.

• Asian-Australasian Journal of Animal Sciences
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• 제32권10호
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• pp.1483-1490
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• 2019

Objective: To explore the molecular mechanisms of fat metabolism and deposition in pigs, an experiment was conducted to identify hepatic mRNAs and miRNAs expression and determine the potential interaction of them in two phenotypically extreme pig breeds. Methods: mRNA and miRNA profiling of liver from 70-day Jinhua (JH) and Landrace (LD) pigs were performed using RNA sequencing. Blood samples were taken to detect results of serum biochemistry. Bioinformatics analysis were applied to construct differentially expressed miRNA-mRNA network. Results: Serum total triiodothyronine and total thyroxine were significantly lower in Jinhua pigs, but the content of serum total cholesterol (TCH) and low-density lipoprotein cholesterol were strikingly higher. A total of 467 differentially expressed genes (DEGs) and 35 differentially expressed miRNAs (DE miRNAs) were identified between JH and LD groups. Gene ontology analysis suggested that DEGs were involved in oxidation-reduction, lipid biosynthetic and lipid metabolism process. Interaction network of DEGs and DE miRNAs were constructed, according to target prediction results. Conclusion: We generated transcriptome and miRNAome profiles of liver from JH and LD pig breeds which represent distinguishing phenotypes of growth and metabolism. The potential miRNA-mRNA interaction networks may provide a comprehensive understanding in the mechanism of lipid metabolism. These results serve as a basis for further investigation on biological functions of miRNAs in the porcine liver.

• Asian-Australasian Journal of Animal Sciences
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• 제33권5호
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• pp.696-703
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• 2020

Objective: Cattle were some of the first animals domesticated by humans for the production of milk, meat, etc. Long noncoding RNA (lncRNA) is defined as longer than 200 bp in nonprotein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle. The purpose of this study is to analyze the characteristics of lncRNA according to sex in Hanwoo cattle. Methods: This study was conducted using the skeletal muscles of 9 Hanwoo cattle include bulls, steers and cows. RNA was extracted from skeletal muscle of Hanwoo. Sequencing was conducted using Illumina HiSeq2000 and mapped to the Bovine Taurus genome. The expression levels of lncRNAs were measured by DEGseq and quantitative trait loci (QTL) data base was used to identify QTLs associated with lncRNA. The python script was used to match the nearby genes Results: In this study, the expression patterns of transcripts of bulls, steers and cows were identified. And we identified significantly differentially expressed lncRNAs in bulls, steers and cows. In addition, characteristics of lncRNA which express differentially in muscles according to the sex of Hanwoo were identified. As a result, we found differentially expressed lncRNAs according to sex were related to shear force and body weight. Conclusion: This study was classified and characterized lncRNA which differentially expressed by sex in Hanwoo cattle. We believe that the characterization of lncRNA by sex of Hanwoo will be helpful for future studies of the physiological mechanisms of Hanwoo cattle.