• BMB Reports
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• 제50권4호
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• pp.201-207
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• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.

• Journal of Microbiology and Biotechnology
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• 제9권5호
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• pp.568-571
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• 1999

Aspergillus oryzae U1521, which was a genetically engineered strain, produced 1,000,600 U per g . glucose of extracellular alkaline protease within 72 h in a submerged fermentation. However, the alkaline protease was not detected during the first 24 h. Northern blot analysis indicated that the enzyme synthesis was repressed at the transcriptional level during the lag period. Both catabolite repression and pH of the growth medium significantly affected the enzyme production. Use of this enzyme as a silver recovery agent from used X-ray film was confirmed by experiments in the shake-flask scale.

• 한국미생물·생명공학회지
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• 제21권3호
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• pp.229-238
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• 1993

An nlp (Ner like protein) gene from E. coli was previously cloned and sequenced. Here we show that expression of the sugar metabolism related genes, lacZ, malQ and malP, increased 2.5-to 8.3-fold in the presence of a plasmid containing the nlp gene. This suggested that the nlp gene could induce maltose- and lactose-metabolism coordinately with crp*1 in the absence of cAMP. Using the nlp-lacZ fusion gene, it was possible to show the promoter of nlp was active in vivo.

• Journal of Microbiology
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• 제34권1호
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• pp.54-60
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• 1996

Taking advantage of the heat inducible HSP82 gene in yeast, chromatin structure after transcription cessation was investigated. Alteration of chromating conformation within the HSP82 gene transcription unit into an active state has been shown to correlate with its transcriptional induction. It was thus of interest to examine whether the active chromatin state within the HSP82 mRNA analysis, the gene ceased its transcription within a few hours of cultivation at a normal condition after heat induction. In this condition, an active chromatin conformation in the HSP82 gene body was changed into an inactie state which was revealed by DNase I resistance and by typical nucleosomal cutting periodicity in the corresponding chromatin. These results thus ruled out the possibility of a long-term maintenance of the DNase I sensitive chromatin after transcription cessation. DNA replication may be a critical event for the chromatin reprogramming.

• Journal of Microbiology and Biotechnology
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• 제21권3호
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• pp.252-255
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• 2011

Both Escherichia coli (E. coli) and Salmonella enterica serovar Typhimurium (S. Typhimurium) have a tdc operon that encodes enzymes involved in a metabolic pathway for the degradation of L-serine and L-threonine. However, S. Typhimurium does not have the tdcR gene, which is a positive regulator in E. coli. In the present study, transcriptional analysis revealed that tdcA expression in E. coli is higher under anaerobic than aerobic growth conditions, but the opposite is true in S. Typhimurium. Interestingly, a tdcR mutant strain of E. coli showed a similar expression pattern to that observed in S. Typhimurium and was also induced by anaerobic shock. These results suggest that the induction of tdcA expression by anaerobic conditions is observable when tdcA expression is low owing to the absence of TdcR.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.125-126
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• 2006

NimbleGen has developed strategies to use its high-density oligonucleotide microarray platform (385,000 probes per array) to map both promoter binding sites and copy number variation at very high-resolution in the human genome. Here we describe a genome-wide map of active promoters determined by experimentally locating the sites of transcription imitation complex binding throughout the human genome using microarrays combined with chromatin immunoprecipitation. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Microarray-based comparative genomic hybridisation (CGH) is animportant research tool for investigating chromosomal aberrations frequently associated with complex diseases such as cancer, neuropsychiatric disorders, and congenital developmental disorders. NimbleGen array CGH is an ultra-high resolution (0.5-50 Kb) oligo array platform that can be used to detect amplifications and deletions and map the associated breakpoints on the whole-genome level or with custom fine-tiling arrays. For whole-genome array CGH, probes are tiled through genic and intergenic regions with a median probe spacing of 6 Kb, which provides a comprehensive, unbiased analysis of the genome.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.49-49
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• 2003

BldD is one of a set of morphological differentiation regulators in Streptomyces coelicolor. The bldD coding region was cloned and heterologously expressed in Escherichia coli. Previous analysis showed the splitting appearance of purified BldD.

• 약학회지
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• 제43권1호
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• pp.42-47
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• 1999

Phorbol ester, growth factors activities are mediated by unclear transcription factors, the c-Fos and c-Jun, which can regulate transcriptional activation through specific DNA sites and by forming the transcription factor AP-l, which usually mediates cell proliferation and differentiation signals. We explored effects of Pini Folium extract (API-l) on AP-l activity. Western blot analysis confirmed that API-l decreased levels of c-Fos or c-Jun protein induced by the tumor promoter Phorbol 12-myristate 13-acetate (PMA; 200 nM). Transient transfection assays with a c-fos promoter reporter construct showed that API-l decreased transcription activity by ore than 50~60%. However, treatment of API-l activity studied further. The main substances were fractionated into dichloromethane layer. Futhermore, API-l extract repressed the [$^3H$]-thymidine uptake in C6 glioma cells, indicating that this extract could be included in a new type of modulator in the mitogenesis.

• Journal of Microbiology
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• 제39권2호
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• pp.109-115
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• 2001

Salmonella typhimurium possesses a cad operon, which contributes to an adaptive response against an acidifying environment. In Escherichia coli, the activation of the cad operon is dependent on cadC, which is located upstream of the operon. However, the activator of cad operon in S. typhimurium has not been known until now. In this study, we selected a putative cadC mutant by trasposon mutagenesis and cloned the cadc of S. typhimurium. Moreover, the cadC mutant was complemented by cadC clone. The cadC gene from S. typhimurium LT-2 consists of 1539 bp encoding a polypeptide ob 512 amino acids, and shows sequence similarity to cadC of E. coli with 53% identity and 67% similarity. The hydrophobicity profile of th S. typhimurim CadC sequence is very similar to E. coli CadC.

• Journal of Microbiology
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• 제40권2호
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• pp.173-177
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• 2002

In order to identify Yawowia lipolytica genes induced by serum, cDNA representational difference analysis was performed using a PCR-select CDNA subtraction method. One of the genes cloned from the subtraction was a gene (YIMBFl) homologous to Saccharomyces cerevisiae MBF1 encoding the coactivator multiprotein bridging factor 1. Disruption of YIMBFl revealed that the gene was net essential for viability, and the Ylmbf△ strain did not show any distinct phenotypic change on solid serum medium. In liquid medium, however. a difference was found in the ability to maintain hyphae induced by serum. This result suggests that the YIMbf1 protein may mediate transcriptional activation of certain genes involved in the hypha fonmation of Y. lipolytica.