• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.769-771
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• 2003

PromSearch는 DNA 염기서열 상에서 프로모터의 위치를 예측하는 프로그램이다. 다루는 대상은 인간 DNA의 프로모터이며, 프로모터의 TSS(transcription start site, 전사시작지점)를 예측하는 것을 목표로 한다. 프로모터 영역을 세분하여 각 영역에 대한 프로파일을 PWM(position weight matrix)을 이용해 작성하며, 임의의 염기서열이 입력으로 주어지면 세분한 영역의 점수를 신경망을 이용해 통합하여 프로모터 여부와 TSS의 위치를 결정한다. 프로모터 영역의 분할은 코어 프로모터의 구성 요소인 TATA-box와 Inr, DPE(downstream promoter element), 그리고 코어 프로모터의 위쪽으로 150bp 크기의 영역 등으로 4분할하였다. Fickett의 데이터를 이용한 평가 결과 sensitivity 43%, specificity 88fp(1/376bp)의 성능을 보였다.

• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.340-342
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• 2004

Promsearch는 인간 DNA에서 코어 프로모터 영역을 예측하는 프로그램이며, PWM(position weight matrix)과 신경망을 기반으로 전사시작지점을 예측한다. 프로그램은 대량의 서열 데이터를 처리할 수 있도록 구성되었으며, 본 논문에서는 인간 염색체 22번에 대한 프로모터 예측 결과를 제시한다. Annotated된 936개의 유전자와 Promsearch가 예측한 프로모터간의 위치의 상관관계를 계산한 결과 87개에 대해 프로모터 예측 결과가 의미 있는 것으로 밝혀졌다. 예측의 민감도는 25%이며, Promsearch가 대규모 시퀀싱 프로젝트에서 나오는 대량의 서열 데이터를 1차적으로 분석하는 도구로서 사용될 수 있음을 확인하였다.

• KSBB Journal
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• v.11 no.4
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• pp.431-437
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• 1996

The nar promoter of Escherichta coli, which is maximally induced under anaerobic conditions in the presence of nitrate, was characterized to see whether the nar promoter cloned onto pBR322 can be used as an expression promoter. The modified nar promoter, in which several bases in the -10 region was mutated to the consensus sequence by site-directed mutagenesis, was characterized in E. coli, on which chromosome the fnr gene affecting expression of the nar promoter according to dissolved oxygen level was mutated. The E. coli lacZ gene was used as a reporter gene. The following effects were investigated to find optimal conditions to induce the modified nar promoter: induction methods, optimal nitrate concentrations, the amount of ${\beta}$-galactosidase expressed at the different growth conditions, and induction characteristics. The following results were obtained from the experiments : expression of ${\beta}$-galactosidase from the modified nar promoter was not affected much by nitrate concentrations. The maximal specific ${\beta}$-galactosidase activity was obtained when E. coli was grown under aerobic conditions, and then the modified nar promoter was induced at OD600=2.2 under microaerobic conditions (DO=1∼2%), under which conditions the maximal specific ${\beta}$-galactosidase activity was 13,000 Miller units. However, the specific ${\beta}$-galactosidase activity was approximately 6,000 Miller units even before the modified nar promoter was induced. Therefore, the modified nar promoter seemed to be useful when the cloned gene wants to be expressed in E. coli constitutively.

• Korean Journal of Poultry Science
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• v.50 no.4
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• pp.261-266
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• 2023

The skeletal muscles of livestock play a crucial role as protein sources for humans, and the consumption of poultry meat is steadily increasing worldwide. Numerous genes, including myogenic regulatory factors, are involved in myogenesis, and precise regulation of them is essential. In this study, genes specifically expressed in muscles were selected, and their promoters were cloned and analyzed. The analysis of gene expression in various tissues of animals revealed that many genes exhibited specific expression patterns in skeletal muscles, with TNNT3, TNNC2, and MYF6 genes showing similar patterns in poultry. The promoter regions of three genes were amplified by polymerase chain reaction to sizes of 1.2 kb, 1.03 kb, and 1.43 kb, respectively. These fragments were then inserted at the front of the enhanced green fluorescent protein gene in vectors. It was confirmed that the sequences of three promoters closely matched the chicken genome sequences. Upon introducing vectors with each promoter into QM7 quail muscle cells, all three promoters successfully induced the expression of the green fluorescent protein. The brightness of the green fluorescence in each promoter was approximately seven times dimmer compared to the control, CMV-IE promoter. It is predicted that more than 230 transcription factors can bind to each promoter, especially various transcription factors expressed in muscles, including myogenic regulatory factors such as MYF5, MYOD, and MYOG. These promoters can be valuable for studying gene expression in poultry muscle cells, and further research is needed to precisely investigate the regulatory region of gene expression in promoters.

• Microbiology and Biotechnology Letters
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• v.35 no.3
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• pp.184-190
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• 2007

Approximately 2.0 kb of the promoter region of the Pichia pastoris phosphoglycerate kinase gene (PGK1) was reduced to a 266 bp fragment and this minimized portion was used for construction of a new episomal constitutive expression vector in P. pastoris. As an approach to developing a constitutive expression vector in P. pastoris, the GAP promoter region of the Pichia expression vector pGAPZB was replaced with sequentially deleted PGK1 promoter fragments fused to a beta-galactosidase gene. When a lacZ gene was used as a reporter gene, PGK1 promoter strength was lower than that of the constitutive GAP promoter but it was higher than TEF1. We report here the development of the pPGKZ-E vector as a new episomal expression vector for heterologous gene expression by removing non-essential regions of the PGK1 promoter. This broadens the choice of episomal expression vectors for controlled constitutive expression in P. pastoris.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2006.11a
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• pp.80-81
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• 2006

닭의 유전자 지도가 밝혀지고 그와 관련한 생물학적 연구들이 활발히 이루어지면서 닭을 생체 반응기나 질병 모델 동물로 이용하기 위한 연구가 많이 진행되고 있다. 이 중 닭을 생체 반응기로 이용하기 위해서는 많은 양의 단백질을 생산하는 난관에 대한 연구가 필수적이다. In vivo와 in vitro에서 난관 특이적 프로모터에 의한 외래 유전자의 발현에 대한 연구를 하였고 유전자를 전이하는 방법으로는 렌티 바이러스 시스템을 이용하였으며, 프로모터는 난관 특이적 프로모터인 오브알부민 프로모터 (5‘ 조절 부분의 1.4kb)와 RSV 프로모터를 이용하였다. 리포터 유전자로는 형광발현 단백질 (enhanced green fluorescence protein, EGFP)을 이용해서 마우스 배아 섬유아세포, 닭 배아 섬유아세포, 난관 상피 세포에서 발현을 유도해서 조직 특이적 발현 여부를 확인하였다. 그 결과 RSV 프로모터는 모든 세포에서 발현하였으나, 오브알부민 프로모터에 의한 리포터 유전자의 발현은 난관 상피 세포에서는 특이적으로 발현하였다. 이와 같은 연구는 산란계를 이용해서 난관으로부터 효율적인 생리 활성 물질을 생산하기 위한 가능성을 보여주었다.

• Journal of Life Science
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• v.18 no.10
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• pp.1395-1399
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• 2008

We have recently reported the PRC1 promoter as a promoter candidate to control expression of transcriptionally targeted genes for breast cancer gene therapy. We tested whether the PRC1 promoter could be also applied for the lung cancer gene therapy. In the transient transfection assay with naked plasmids containing the luciferase fused to the PRC1 promoter, the promoter showed little activity in the normal lung cell line, MRC5. However, in the lung cancer A549 cells, PRC1 showed approximately 30-fold activation which was similar to the survivin promoter, the gene whose promoter has been already reportedas a candidate for the gene therapy of lung cancer. In viral systems, the PRC1 promoter showed approximately 75% and 66% of transcriptional activity compared to the CMV promoter in the adeno-associated virus (AAV) and the adenovirus (AV) systems, respectively. However, the PRC1 promoter in either AAV or AV showed approximately 20% activity compared to the CMV promoter in the normal lung cells. In addition, human lung tumor xenograft mice showed that the PRC1 promoter activity was as strong as the CMV activity in vivo. Taken together, these results suggested that PRC1 might be a potential promoter candidate for transcriptionally targeted lung cancer gene therapy.

• Korean Journal of Microbiology
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• v.31 no.4
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• pp.267-273
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• 1993

We screened promoters inducible by superoxide radical from Escherichia coli. For this. we constructed random promoter library from E. coli MG 1655 using a promoter-probing plasmid. pJAC4. Six hundred and sixty clones in this library were classified based on their promoter strength by ampicillin gradient plate assay. Three hundred and eighty three clones with relatively weak to medium promoter strength were selected and then screened for their inducibility by superoxide radical on ampicillin gradient plate containing paraquat. Three clones (clones 5. 15 and 34) were detected to be induced by paraquat treatment and the level of induction were between 1.4 and 4 folds. Comparison of nucleotide sequences of the cloned promoter fragment with registered sequences in GENBANK and EMBL databases suggests that the cloned DNA fragments have not been yet characterized in E. coli. Transcription start sites in these clones were determined by rrimer extension and S I nuclease protection analysis. S 1 analysis of clones 5 and IS indicated that the mRNA levels were increased by paraquat treatment. Especially. clone 5 \vas found to have two transcription start sites. the upstream start site of which was selectively used by paraquat treatment. Searching for promoter clements. we found that only the downstream promoter of clone 5 has -10 and - 35 promoter elements recognized by RNA polymerase ($E\sigma^{70}$) and the others have no conserved promoter elements. This suggests that these superoxideinducible promoters may require transcription initiation protein(s) other than $E\sigma^{70}$.

• Proceedings of the IEEK Conference
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• 2003.07d
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• pp.1569-1572
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• 2003

최근 생명공학 분야의 기술이 혁신적으로 발달함에 따라 게놈 프로젝트가 본래 계획보다 2년 앞당겨져 2003 년 4 월 인간 유전자의 완전한 서열을 밝히고 성공적으로 완료됨으로서 관련 연구자들은 인간의 유전자에 대한 대량의 서열 데이터를 얻게 되었다. 그래서 게놈 프로젝트의 다음 단계로서 엄청난 양의서열 정보 분석으로부터 유전자의 기능을 파악하고자 하는 연구들이 이미 세계적으로 활발히 진행되고 있다. 이러한 연구들의 최종적 목표는 질병 치료와 생명연장의 실현이라고 볼 수 있다. 유전자 연구를 위해선 우선 일차적으로 유전자 부위를 파악해야 한다. 유전자는 구조적으로 다시 여러 부분으로 나뉘는데 유전자 발현의 개시에 매우 중요한 요소 중 하나가 바로 프로모터 (Promoter) 이다. 프로모터 내에는 TATA box 가 있는데 이는 프로모터의 핵심 요소이다. 프로모터는 생명체의 종 그리고 RNA 중합효소의 종류에 따라 다르다. 이 논문에서는 다양한 신경망 알고리즘 중의 하나인 Backtpropagation 을 이용하여 밝혀지지 알은 서열에서 인간을 포함하는 원핵생물의 프로모터 서열을 예측할 수 있는 방법을 얻었기에 소개하고자 한다.

• Journal of Applied Biological Chemistry
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• v.64 no.1
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• pp.39-48
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• 2021

Droughts are one of the abiotic stresses that hinders the growth and productivity of crop plants. Coping with abiotic stress is necessary to understand the molecular regulatory networks that makes plants respond to adverse environmental conditions. In our experiment to find a combination that can cope with abiotic stress (respond to drought), we screened 5 stress-inducible promoters that are expressed only under stress conditions. This founded 36 cis-elements in stress-inducible promoters. With the result we designed 2 synthetic promoters (BL1, BL2) for fine-controlled regulation by assembling cis-elements from the native promoters, which are expressed only under stress caused by droughts. Analysis of the transgenic plant (BL1-GUS, BL2-GUS) showed that the synthetic promoters increased the expression of β-glucuronidase (GUS) in transgenic plants under desiccation. Also in the transient activation assay demonstrated that synthetic promoters induced the co-transformation of effector DREB1A and DREB2C. These results expect that the synthetic promoter with a combination of drought-specific elements can be used to respond to various abiotic stress and is resistant to stress without causing growth retardation.