유전자의 발현 조절 관련 연구의 현황과 미래 교육과정

유금복,김성경,전상학 한국현장과학교육학회 2018 현장과학교육 Vol.12 No.4

Modern science and technology has been growing remarkably, especially in the field of genetics, which is called 'genetic revolution'. In order to cultivate creative talents in the field of science and technology, it is necessary to deeply think about how to bring new scientific discoveries and academic progress into the curriculum. In this paper, we first looked at the meaning of genomic equivalence and the importance of regulation of gene expression. We then reviewed how the curriculum handled the regulation of gene expression. Finally, for future curriculum, we reviewed the recent trends of research on the regulation of gene expression at the level of RNA. The genetic equivalence inevitably invoked the importance of regulation of gene expression. To date, the curriculum has handled the regulation of gene expression at the level of the transcriptional level in prokaryotes and eukaryotes. However, recent studies showed that various kinds of RNAs, which include miRNA, siRNA, crRNA and lncRNA, play important roles in the regulation of gene expression and their abnormal function could cause disease. In addition, these RNAs are used today as a very useful tool for studying regulation of gene expression and especially crRNA for gene editing. Research on regulation of gene expression has not only high scientific value but also a great social impact. Therefore, for an in-depth and integrated understanding of scientific literacy and life phenomena, it is necessary to consider including the RNA world in terms of regulation of gene expression in the future curriculum. 현대의 과학기술은 눈부신 성장을 거듭하고 있으며, 특히 유전학 분야는 ‘유전자 혁명’이라고 불릴 만큼 획기적인 발전이 이루어지고 있다. 과학기술 분야에서 창의력을 갖춘 인재 양성을 위해서는, 새로운 과학적 발견과 학문적 발전을 어떻게 교육과정에 담아낼 것인가에 대한 깊은 고민을 필요로 한다. 본 논문에서는 유전체 등가성의 의미와 업적을 살펴보고 교육과정 변천에 따라 유전자 발현 조절의 내용 요소가 어떻게 반영되었는지 알아보았다. 마지막으로 유전자 발현 조절 분야의 최근 연구 성과를 소개하고, 이러한 성과를 미래의 교육과정에 도입하는 것의 의미를 살펴보았다. 유전체 등가성의 증명으로부터 유전자 발현 조절의 중요성이 제기되었고, 이를 밝히기 위한 연구가 계속되고 있다. 과학과 교육과정에서도 유전자 발현 조절의 중요성을 인식하고, 연구 내용을 교육과정에 담기 위해 지속적으로 노력해왔다. 최근 유전자의 전사 후 조절 과정에서 중요한 역할을 하고 있는 다양한 종류의 RNA들이 발견됨에 따라, 유전자 발현 조절에 대한 연구의 중요성과 가치가 더욱 커지고 있다. 유전자 발현 조절에 대한 연구는 매우 중요한 과학적 의미를 가질 뿐 아니라 사회적으로 미치는 영향도 매우 크다. 따라서 과학적 소양의 함양과 생명 현상에 대한 심층적이고 통합적인 이해를 위하여, 교육과정에 유전자발현 조절과 관련하여 RNA 세계에 대한 내용을 추가 도입하는 것을 고려할 필요가 있다.

An Improved Tet-on System to Tightly Conditionally Regulate Reporter Gene Expression

Yanping Ren,Xiangping Li,Qingyou Liu,Yanfei Deng,Deshun Shi 한국생물공학회 2015 Biotechnology and Bioprocess Engineering Vol.20 No.1

Reporter genes are often used as markers totrack the integration and expression of target genes inanimal genetic engineering. To avoid potential side effectsfrom reporter genes, in this study an improved Tet-onsystem was developed to control reporter gene expression,and its effectiveness was explored in transgenic cells. First,the rtTA protein was fused with Tat and NLS proteins toobtain the prokaryotic expression vector pET32a-Tat-rtTANSL. A eukaryotic transgenic vector was constructed, p-HS4-BPA-TmA-HS4, in which the reporter (mCherry) andtarget (PRL) genes were promoted by TRE and BCN,respectively. After confirming the functionality of thetransgenic vector, purified rtTA protein and Dox wereadded to induce expression of the mCherry gene. Theoptimal amount of purified rtTA protein, its influence ontarget gene expression, and the time of rtTA protein actionwere each investigated separately. The results showed thatrtTA protein was expressed in transformed E. coli with IPTGinduction. TRE could promote mCherry gene expressionby co-transfecting the constructed transgenic vector andprtTA plasmid. When purified rtTA protein and Dox wereadded, red fluorescence was observed in Bcap-37 cellstransfected with the p-HS4-BPA-TmA-HS4 vector, and theexogenous PRL gene was expressed regardless of mCherrygene expression. The optimal amount of rtTA protein was16 μg/mL, and it needed about 6 h to promote mCherrygene expression in transfected cells. These resultsdemonstrate that the expression of the mCherry reportergene can be tightly and conditionally regulated by our Tetonsystem.

GeneNetFinder2: Improved Inference of Dynamic Gene Regulatory Relations with Multiple Regulators

Kyungsook Han,Jeonghoon Lee IEEE 2016 IEEE/ACM transactions on computational biology and Vol.13 No.1

<P>A gene involved in complex regulatory interactions may have multiple regulators since gene expression in such interactions is often controlled by more than one gene. Another thing that makes gene regulatory interactions complicated is that regulatory interactions are not static, but change over time during the cell cycle. Most research so far has focused on identifying gene regulatory relations between individual genes in a particular stage of the cell cycle. In this study we developed a method for identifying dynamic gene regulations of several types from the time-series gene expression data. The method can find gene regulations with multiple regulators that work in combination or individually as well as those with single regulators. The method has been implemented as the second version of GeneNetFinder (hereafter called GeneNetFinder2) and tested on several gene expression datasets. Experimental results with gene expression data revealed the existence of genes that are not regulated by individual genes but rather by a combination of several genes. Such gene regulatory relations cannot be found by conventional methods. Our method finds such regulatory relations as well as those with multiple, independent regulators or single regulators, and represents gene regulatory relations as a dynamic network in which different gene regulatory relations are shown in different stages of the cell cycle. GeneNetFinder2 is available at http://bclab.inha.ac.kr/GeneNetFinder and will be useful for modeling dynamic gene regulations with multiple regulators.</P>

C1q and TNF related protein 1 regulates expression of inflammatory genes in vascular smooth muscle cells

김도우,박승윤 한국유전학회 2019 Genes & Genomics Vol.41 No.4

Background C1q and TNF related protein 1 (C1QTNF1) is known to be associated with coronary artery diseases. However, the molecular function of C1QTNF1 on the vascular smooth muscles remains to be investigated. Objective This study was therefore undertaken to investigate the effect of C1QTNF1 on gene expression of human smooth muscle cells and to reveal potential molecular mechanisms mediated by C1QTNF1. Methods Vascular smooth muscle cells were incubated with recombinant C1QTNF1 for 16 h, followed by determining any change in mRNA expressions by Affymetrix genechip. Gene ontology (GO), KEGG pathway, and protein–protein interaction (PPI) network were analyzed in differentially expressed genes. In addition, validation of microarray data was performed using quantitative real-time PCR. Results The mRNA expressions of annotated 74 genes were significantly altered after incubation with recombinant C1QTNF1; 41 genes were up-regulated and 33 down-regulated. The differentially expressed genes were enriched in biological processes and KEGG pathways associated with inflammatory responses. In the PPI network analysis, IL-6, CCL2, and ICAM1 were identified as potential key genes with relatively high degree. The cluster analysis in the PPI network identified a significant module composed of upregulated genes, such as IL-6, CCL2, NFKBIA, SOD2, and ICAM1. The quantitative real-time PCR results of potential key genes were consistent with microarray data. Conclusion The results in the present study provide insights on the effects of C1QTNF1 on gene expression of smooth muscle cells. We believe our findings will help to elucidate the molecular mechanisms regarding the functions of C1QTNF1 on smooth muscle cells in inflammatory diseases.

Exploring Trans-acting regulators of gene expression associated with metabolic syndrome: a coupled application of factor analysis and linkage analysis

김기주,민진영,김경아,성주헌,조성일 한국유전학회 2013 Genes & Genomics Vol.35 No.1

Metabolic syndrome is an established public health problem because it increases the risk of cardiovascular disease. Although many genes contribute to the etiology of metabolic syndrome, the effect size of each gene is much weaker than predicted by heritability. Exploring the regulation of gene expression levels can bridge this gap. Here, we aimed to explore genomic loci for a transregulator of gene expression associated with metabolic syndrome via factor analysis and linkage analysis. Fortynine gene-expression quantitative traits (eQTs) associated with metabolic syndrome were selected and clustered into three latent eQTs by factor analysis. These included insulin-related, lipid-related, and glucose-related latent eQTs. Linkage analyses were performed for 49 original eQTs and 3 latent eQTs. Two original eQTs, adipose differentiationrelated protein and IRS2, showed the highest LOD scores (3.09 and 3.08, respectively). We observed that the insulinrelated and the lipid-related latent eQTs had stronger linkage evidence than the original eQTs, suggesting the presence of common gene regulators captured as latent eQTs. Several single nucleotide polymorphism markers located on the peaks were co-localized with specific genes. Five of them were related to the neuronal system, which plays a role in the metabolic syndrome pathway. The findings related those eQTs could contribute to our understanding regarding the genetic pathway for insulin and lipid metabolism, particularly the regulation of gene expression.

유전자 상호발현 조절을 통한 에탄올 내성 메커니즘의 규명

정회명(Hoe-Myung Jung),최호정(Ho-Jung Choi),남수완(Soo-Wan Nam),전숭종(Sung-Jong Jeon),김연희(Yeon-Hee Kim) 한국생명과학회 2016 생명과학회지 Vol.26 No.1

에탄올은 산업적으로 매우 가치 있는 물질이지만, 효모세포에 있어서 에탄올의 축적은 세포 독성과 목적산물의 생산성을 감소시키는 스트레스원이다. 따라서 효모세포에 있어서 에탄올 내성의 증가는 에탄올 생산성 증대와 밀접한 관계가 있는 중요한 요소라고 할 수 있다. 본 연구에서는 에탄올 내성을 증가시키기 위해 YDJ1과 PEP5 유전자를 목적 유전자로 선정하여 이들 유전자의 과발현과 과발현에 따른 상호발현조절을 분석하여 에탄올 내성 메커니즘의 일부를 해명하고자 한다. YDJ1과 PEP5 유전자를 ADH1 promoter 하류에 연결시켜 pA-YDJ1과 pA-PEP5 plasmid를 구축하고 각각 BY4742, BY4742△ydj1와 BY4742△pep5 균주에 도입하였다. YDJ1과 PEP5 유전자의 과발현에 의해서 BY4742△ydj1/pA-YDJ1과 BY4742△pep5/pA-PEP5 균주의 에탄올내성이 숙주세포의 수준까지 회복되었음을 확인 할 수 있었다. 이 두 유전자의 상호발현조절을 조사하기 위해, BY4742△ydj1△pep5 균주에서 YDJ1과 PEP5 유전자의 과발현을 시도해본 결과, BY4742△ydj1△pep5/pA-YDJ1, pA-PEP5 균주의 경우, 8% 에탄올 배지에서 BY4742 균주의 약 90%정도 까지 에탄올 내성이 회복됨을 확인하였다. BY4742△ydj1△pep5/pA-YDJ1, pA-PEP5 균주에서 YDJ1 유전자는 PEP5 유전자의 과발현을 더욱더 유도하여 에탄올 내성을 증가시켰으며, 이는 YDJ1 유전자가 PEP5 유전자의 상위에서 발현을 부분적으로 조절한다고 생각 할 수 있다. Ethanol is a very valuable material, however, it is also a source of stress, as the accumulation of ethanol in a medium inhibits cell viability and decreases productivity of the target product. Therefore, the ethanol tolerance of yeast, which is closely related to ethanol productivity, is an important factor in industrial ethanol production. In this study, the YDJ1 and PEP5 genes were selected as target genes for elucidating ethanol-tolerant mechanisms by analyzing the expression regulation of these genes. The pA-YDJ1 and pA-PEP5 plasmids containing YDJ1 and PEP5 genes under an ADH1 promoter, respectively, were constructed and transformed into BY4742 (host strain), BY4742△ydj1, and BY4742△pep5 strains. The ethanol tolerance in the BY4742△ydj1/ pA-YDJ1 and BY4742△pep5/pA-PEP5 transformants was restored by overexpression of the YDJ1 and PEP5 genes to the host strain level. The YDJ1 and PEP5 genes were also introduced into the double gene disruptant (BY4742△ydj1△pep5) to investigate the expression regulation of the YDJ1 and PEP5 genes. The simultaneous overexpression of the YDJ1 and PEP5 genes restored ethanol tolerance to the 90% level of the BY4742 strain under 8% ethanol stress. The YDJ1 gene induced more overexpression of the PEP5 gene in the BY4742△ydj1 △pep5/pA-YDJ1, pA-PEP5 strain, suggesting that the YDJ1 gene partially regulates the expression of the PEP5 gene as an upstream regulator.

Drug Similarity Search Based on Combined Signatures in Gene Expression Profiles

차기훈,김민성,오기민,신현정,이관수 대한의료정보학회 2014 Healthcare Informatics Research Vol.20 No.1

Objectives: Recently, comparison of drug responses on gene expression has been a major approach to identifying the functional similarity of drugs. Previous studies have mostly focused on a single feature, the expression differences of individual genes. We provide a more robust and accurate method to compare the functional similarity of drugs by diversifying the features of comparison in gene expression and considering the sample dependent variations. Methods: For differentially expressed gene measurement, we modified the conventional t-test to normalize variations in diverse experimental conditions of individual samples. To extract significant differentially co-expressed gene modules, we searched maximal cliques among the co-expressed gene network. Finally, we calculated a combined similarity score by averaging the two scaled scores from the above two measurements. Results: This method shows significant performance improvement in comparison to other approaches in the test with Connectivity Map data. In the test to find the drugs based on their own expression profiles with leave-one-out cross validation, the proposed method showed an area under the curve (AUC) score of 0.99, which is much higher than scores obtained with previous methods, ranging from 0.71 to 0.93. In the drug networks, we could find well clustered drugs having the same target proteins and novel relations among drugs implying the possibility of drug repurposing. Conclusions: Inclusion of the features of a co-expressed module provides more implications to infer drug action. We propose that this method be used to find collaborative cellular mechanisms associated with drug action and to simply identify drugs having similar responses.

The Reduced Form of Coenzyme Q10 Decreases the Expression of Lipopolysaccharide-Sensitive Genes in Human THP-1 Cells

Constance Schmelzer,Christine Kohl,Gerald Rimbach,Frank Döring 한국식품영양과학회 2011 Journal of medicinal food Vol.14 No.4

Monocytes are key players in inflammatory processes that are triggered by lipopolysaccharide (LPS), the major outer membrane component of Gram-negative bacteria. The present study in human monocytic THP-1 cells was designed in order to identify LPS-inducible genes that are down-regulated by the reduced form of coenzyme Q_10 (ubiquinol, Q_10H_2). For this purpose, THP-1 cells were incubated with 10 μM Q_10H_2 for 24 hours. Subsequently, cells were stimulated for 4 hours with 1 μg/mL LPS, and the resulting gene expression levels were determined using microarrays. Fourteen LPS-inducible genes were identified to be significantly (P ≤ .05) down-regulated by Q_10H_2 pretreatment between a factor of 1.32 and 1.65. The strongest effect of Q_10H_2 incubation was found for the nuclear receptor coactivator 2 gene (NCOA2). Gene ontology terms revealed for the Q10H2-sensitive genes an involvement in, e.g., signal transduction processes (centaurin, delta 1; NCOA2; pleckstrin and Sec7 domain containing 3; protein phosphatase 2, regulatory subunit B [B56], γ isoform), transcriptional regulation (NCOA2; POU domain, class 2, transcription factor 1; ETS variant gene 3), and cell proliferation pathways (hypothetical protein FLJ36090, epidermal growth factor receptor pathway substrate 15). In conclusion, we provide evidence in THP-1 cells that Q_10H_2 modulates LPS-induced gene expression.

Expression of peroxiredoxin I regulated by gonadotropins in the rat ovary

Lee, Yu-Il,Kang, Woo-Dae,Kim, Mi-Young,Cho, Moon-Kyoung,Chun, Sang-Young The Korean Society for Reproductive Medicine 2011 Clinical and Experimental Reproductive Medicine Vol.38 No.1

Objective: Peroxiredoxins (Prxs) play an important role in regulating cellular differentiation and proliferation in several types of mammalian cells. This report examined the expression of Prx isotype I in the rat ovary after hormone treatment. Methods: Immature rats were injected with 10 IU of pregnant mare's serum gonadotropin (PMSG) to induce the growth of multiple preovulatory follicles and 10 IU of human chorionic gonadotropin (hCG) to induce ovulation. Immature rats were also treated with diethylstilbestrol (DES), an estrogen analogue, to induce the growth of multiple immature follicles. Northern blot analysis was performed to detect gene expression. Cell-type specific localization of Prx I mRNA were detected by in situ hybridization analysis. Results: During follicle development, ovarian Prx I gene expression was detected in 3-day-old rats and had increased in 21-day-old rats. The levels of Prx I mRNA slightly declined one to two days following treatment with DES. A gradual increase in Prx I gene expression was observed in ovaries obtained from PMSG-treated immature rats. Furthermore, hCG treatment of PMSG-primed rats resulted in a gradual stimulation of Prx I mRNA levels by 24 hours (2.1-fold increase) following treatment, which remained high until 72 hours following treatment. In situ hybridization analysis revealed the expression of the Prx I gene in the granulosa cells of PMSG-primed ovaries and in the corpora lutea of ovaries stimulated with hCG for 72 hours. Conclusion: These results demonstrate the gonadotropin and granulosa cell-specific stimulation of Prx I gene expression, suggesting its role as a local regulator of follicle development.

Identification of differentially expressed genes in murine embryos at the blastocyst stage using annealing control primer system

Cui, Xiang-Shun,Shin, Mi-Ra,Lee, Kyung-Ah,Kim, Nam-Hyung Wiley Subscription Services, Inc., A Wiley Company 2005 Molecular reproduction and development Vol.70 No.3

<P>The identification of embryo-specific genes would provide insights into early embryonic development. However, the current methods employed to identify the genes that are expressed at a specific developmental stage are labor intensive and suffer from high rates of false positives. Here we employed a new and accurate reverse transcription-polymerase chain reaction (RT-PCR) method that involves annealing control primers (ACPs) to identify the genes that are specifically or prominently expressed in mouse blastocysts compared to 4-cell stage embryos. Using 120 ACPs, we identified and sequenced 74 of these differentially expressed genes (DEGs). Basic Local Alignment Search Tool (BLAST) searches revealed that 53 were known genes, 9 encoded ribosomal proteins, and 12 were unknown genes. Of the known genes, 14 were selected and further characterized using real-time quantitative PCR to assess their stage-specific expression in mouse embryos. This analysis suggests that the ACP system is a very good method for the identification of stage-specific genes in small numbers of mouse embryos. Further analysis of the differentially expressed blastocyst genes we have identified will provide insights into the molecular basis of preimplantation development. Mol. Reprod. Dev. 70: 278–287, 2005. © 2005 Wiley-Liss, Inc.</P>