• Journal of KIISE:Software and Applications
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• v.30 no.3_4
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• pp.379-387
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• 2003

A lot of microbial genome projects have been completed to pour the enormous amount of genomic sequence data. In this context. the problem of identifying promoters in genomic DNA sequences by computational methods has attracted considerable research attention in recent years. In this paper, we propose a new model of prokaryotic core promoter region including the -10 region and transcription initiation site, that is Dependency-Reflecting Decomposition Model (DRDM), which captures the most significant biological dependencies between positions (allowing for non-adjacent as well as adjacent dependencies). DRDM showed a good result of performance test and it will be employed effectively in predicting promoters in long microbial genomic Contigs.

• 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.

• The Korean Journal of Zoology
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• v.38 no.3
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• pp.433-441
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• 1995

Mammary tissue-specificity of the caprine $\beta$-lactoglobulin promoter appears to be secured by repression in non-expressing cells. In order to identify the mechanism of the negative regulation, the upstream promoter sequence of the caprine $\beta$-lactoglobulin gene was analyzed in detail. The repression was mediated by the upstream flanking sequence from -47O to -205. The sequence could repress the promoter activity of $\beta$-lactoglobulin in either orientation. The effect of the putative negative regulation element of caprine $\beta$-lactoglobulin on heterlogous promoters, however, varied: the promoter activity of herpes simplex virus thimidine kinase was either repressed or activated by the sequence depending on its orientation, while the SV4O early promoter was activated rather than repressed. The regulatory sequence involving the putative negative regulatory element was strongly shifted with the nuclear extract from non-mammary HeLa and CV-1 cells, while only weak shift was observed with that of mammary HC11 cells. Such correlation between repression and factor binding suggests that the protected regions in foot-printing assay may be the negative regulatory elements of $\beta$-lactoalobulin that serve tissue-specific repression.

• 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 $E\sigma^{70}$.

• Journal of KIISE:Software and Applications
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• v.30 no.5_6
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• pp.487-496
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• 2003

The promoter that plays a very important role in gene expression as a signal part has various binding sites for transcription factors. These binding sites are located on various parts in promoter region and have highly conserved consensus sequence patterns. This paper presents a new method for the consensus pattern search in promoter regions using genetic algorithm, which adopts the assumption of N-occurrence-per-dataset model of MEME algorithm and employs the advantage of Wataru method in determining the pattern length. Our method will be employed by genome researchers who try to predict the promoter region on anonymous DNA sequence and to find out the binding site for a specific transcription factor.

• Korean Journal of Microbiology
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• v.47 no.2
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• pp.158-162
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• 2011

Amino acid sequence alignment shows that $\underline{P}$roteus $\underline{m}$irabilis $\underline{t}$ranscription $\underline{r}$egulator (PMTR) has cystein sequence homology at metal binding domain to CueR (copper resistance) protein, which conserves two cysteins (Cys 112 and Cys 120 in PMTR). Gel shift assay revealed that PMTR protein bound to promoter region of Escherichia coli copA (copper-translocating P-type ATPase) and Proteus mirabilis atpase (putative copper-translocating P-type ATPase) genes except that of E. coli zntA (zinc-translocating P-type ATPase) gene. DNase I protection experiment indicated that PMTR protein protected the region over -35 box and close to -10 box. DNase I hypersensitive bases were shown at C and A bases of labeled template strand and at G and C bases of labeled non-template strand of DNA. These hypersensitive bases were appeared in other metalloregulatory proteins of MerR family, which suggests protein-induced DNA bending.

• The Journal of Korean Society of Virology
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• v.26 no.1
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• pp.131-137
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• 1996

The sequences of p10 gene its promoter of Hyphantria cunea NPV were determined. According to the sequence analysis, the putative p10 gene ORF has 285 bp. The 5'-non-coding leader sequence of the p10 gene promoter contained the TATA box and the putative transcription initiation site TAAG motif. Poly (A) tail signals, AATAAA sequence was at site 65 base upstream from the 3' terminus. The deduced amino acid sequence of p10 protein was 95 with a predicted molecular weight of 10.26 kDa. In the p10 protein sequence, a hydrophobic region was present at the N-terminus of the protein, whereas the C-terminus was highly hydrophilic. The p10 protein of H. cunea NPV did not contain cysteine, histidine, trytophan, tryptophane, tyrosine, glutamine and asparagine residues.

• Microbiology and Biotechnology Letters
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• v.17 no.6
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• pp.600-605
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• 1989

For the purpose of isolation of the Zymomonas mobilis DNA fragments showing promoter activity in Escherichia coli, a promoter screening vector, PCMT215 was constructed by transferring a promoterless chloramphenicol acetyltransferase (CAT) gene of pYEJ001 into pMT21 which contains $\beta$-lactamase gene and multiple cloning sites. A library of Z, mobilis Sau3AI DNA fragments was constructed in E. coli using the newly constructed pCMT215. Fourteen clones showing resistance to chloramphenicol ranging in concentration from 30 to 750 $\mu$g/$m\ell$ were selected. From five clones of them, the Z. mobilis DNA fragments expressing CAT gene of the recombinant plasmids were sequenced and then sites of transcriptional initiation were identified. The nucleotide sequences of the cloned DNA shared AT rich regions, poly A's or T's stretches and palindromic regions. The positions of transcriptional initiation for CAT gene occurred at more than one site spaced over by 4 to 190 base pairs on the cloned fragments in E. coli.

• Proceedings of the KIEE Conference
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• 2003.07d
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• pp.2552-2554
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• 2003

난수발생기 (Random generator-RG)와 GRNN을 이용한 분류기 설계방식을 제안하며, 이를 프로모터 염기서열의 분류에 적용한다. 주어진 난수범위에서 다중 분류기를 발생하였으며, 그 성능을 예측정확도와 분류민감도 측면에서 평가하였고, 분류민감도는 다시 전체와 개별적 프로모터에 대해서 세분화하여 평가하였다. 최적화된 분류기 상호간의 비교에서 제안된 기법은 모든 임계점에 대해서, 전체 분류민감도와 전체 예측정확도를 향상시키었으며, 이는 전체 분류 민감도에서 더 두드러졌다. 한편, 개별적 프로모터에 대한 분류민감도와 예측정확도도 평균적으로 향상되었다. 이 같은 결과로 제안된 기법이 분류와 예측성능을 동시에 증진하는데 매우 효과적임을 알 수 있었다.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.9 no.5
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• pp.1218-1224
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• 2008

Located on the upstream of a gene, the promoter region that plays a very important role in the control of gene expression as a signal part has various binding sites for transcription factors. These binding sites are present in various parts of the promoter region and assume an aspect of highly conserved consensus sequence pattern. This paper deals with the introductions of search methods for consensus pattern, including Wataru method, EM algorithm, MEME algorithm, Genetic algorithm and Phylogenetic Footprinting method, and intends to give future prospects of research on this field.