• Interdisciplinary Bio Central
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• v.3 no.2
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• pp.8.1-8.6
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• 2011

Background: Thanks to the development of the mathematical/statistical reverse engineering and the high-throughput measuring biotechnology, lots of biologically meaningful genegene interaction networks have been revealed. Steady-state analysis of these systems provides an important clue to understand and to predict the systematic behaviours of the biological system. However, modeling such a complex and large-scale system is one of the challenging difficulties in systems biology. Results: We introduce a new stochastic modeling approach that can describe gene regulatory mechanisms by dividing two (DNA and protein) layers. Simple queuing system is employed to explain the DNA layer and the protein layer is modeled using G-networks which enable us to account for the post-translational protein interactions. Our method is applied to a transcription repression system and an active protein degradation system. The steady-state results suggest that the active protein degradation system is more sensitive but the transcription repression system might be more reliable than the transcription repression system. Conclusions: Our two layer stochastic model successfully describes the long-run behaviour of gene regulatory networks which consist of various mRNA/protein processes. The analytic solution of the G-networks enables us to extend our model to a large-scale system. A more reliable modeling approach could be achieved by cooperating with a real experimental study in synthetic biology.

• BMB Reports
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• v.52 no.2
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• pp.127-132
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• 2019

Cells must fine-tune their gene expression programs for optimal cellular activities in their natural growth conditions. Transcriptional memory, a unique transcriptional response, plays a pivotal role in faster reactivation of genes upon environmental changes, and is facilitated if genes were previously in an active state. Hyper-activation of gene expression by transcriptional memory is critical for cellular differentiation, development, and adaptation. TREM (Transcriptional REpression Memory), a distinct type of transcriptional memory, promoting hyper-repression of unnecessary genes, upon environmental changes has been recently reported. These two transcriptional responses may optimize specific gene expression patterns, in rapidly changing environments. Emerging evidence suggests that they are also critical for immune responses. In addition to memory B and T cells, innate immune cells are transcriptionally hyperactivated by restimulation, with the same or different pathogens known as trained immunity. In this review, we briefly summarize recent progress in chromatin-based regulation of transcriptional memory, and its potential role in immune responses.

• KSBB Journal
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• v.9 no.3
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• pp.339-345
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• 1994

Deletions between UASG and the GALI TATA box reduced glucose repression and allowed constitutive expression of the gene product in the absence of galactose. The relative inducer level (ratio of galactose/glucose concentrations) affected the extent of gene expression and glucose repression. Glucose repression was reduced by a factor of 2 to 5 as the relative inducer level increased. In the medium containing galactose only, induction of ${\beta}$-galactosidase synthesis by galactose increased with plasmid copy number. On the contrary, plasmid copy number did not affect significantly ${\beta}$-galactosidase synthesis in the medium containing both glucose and galactose (2% glucose＋2% galactose), which might be due to glucose repression caused by high glucose concentration. However, when the medium contained the relatively high inducer level (0.4% glucose＋0.8% galactose), ${\beta}$-galactosidase synthesis increased with plasmid copy number, indicating that the beneficial effect of higher galactose concentration was weaker than the repressive effect of higher glucose concentration.

• BMB Reports
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• v.45 no.10
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• pp.577-582
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• 2012

single-minded (sim) is a master regulatory gene that directs differentiation in the central nervous system during Drosophila embryogenesis. Recent identification of the mesectoderm enhancer (MSE) of sim has led to the hypothesis that two Snail (Sna)-binding sites in the MSE may repress sim expression in the presumptive mesoderm. We provide evidence here that three Sna-binding sites proximal to the sim promoter, but not those of the MSE, are responsible for the mesodermal repression of sim in vivo. Using transgenic embryos injected with lacZ transgenes, we showed that sim repression in the mesoderm requires the three promoter-proximal Sna-binding sites. These results suggest that Sna represses the mesectodermal expression of sim by directly repressing the nearby promoter, and not by quenching adjacent transcriptional activators in the MSE. These data also showed how the MSE, lacking the three proximal Sna-binding sites, reproduced the endogenous pattern of sim expression in transgenic embryos.

• BMB Reports
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• v.49 no.3
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• pp.135-136
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• 2016

Small interfering RNAs (siRNAs) have been developed to intentionally repress a specific gene expression by directing RNA-induced silencing complex (RISC), mimicking the endogenous gene silencer, microRNAs (miRNAs). Although siRNA is designed to be perfectly complementary to an intended target mRNA, it also suppresses hundreds of off-targets by the way that miRNAs recognize targets. Until now, there is no efficient way to avoid such off-target repression, although the mode of miRNA-like interaction has been proposed. Rationally based on the model called "transitional nucleation" which pre-requires base-pairs from position 2 to the pivot (position 6) with targets, we developed a simple chemical modification which completely eliminates miRNA-like off-target repression (0%), achieved by substituting a nucleotide in pivot with abasic spacers (dSpacer or C3 spacer), which potentially destabilize the transitional nucleation. Furthermore, by alleviating steric hindrance in the complex with Argonaute (Ago), abasic pivot substitution also preserves near-perfect on-target activity (∼80-100%). Abasic pivot substitution offers a general means of harnessing target specificity of siRNAs to experimental and clinical applications where misleading and deleterious phenotypes from off-target repression must be considered.

• BMB Reports
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• v.47 no.11
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• pp.619-624
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• 2014

Antisense RNA is a type of noncoding RNA (ncRNA) that binds to complementary mRNA sequences and induces gene repression by inhibiting translation or degrading mRNA. Recently, several small ncRNAs (sRNAs) have been identified in Escherichia coli that act as antisense RNA mainly via base pairing with mRNA. The base pairing predominantly leads to gene repression, and in some cases, gene activation. In the current study, we examined how the location of target sites affects sRNA-mediated gene regulation. An efficient antisense RNA expression system was developed, and the effects of antisense RNAs on various target sites in a model mRNA were examined. The target sites of antisense RNAs suppressing gene expression were identified, not only in the translation initiation region (TIR) of mRNA, but also at the junction between the coding region and 3' untranslated region. Surprisingly, an antisense RNA recognizing the upstream region of TIR enhanced gene expression through increasing mRNA stability.

• Journal of Microbiology and Biotechnology
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• v.3 no.2
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• pp.78-85
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• 1993

In order to elucidate the mechanism which regulates the production of cyclodextrin glucanotransferase (CGTase) and to achieve overproduction of CGTase by releasing catabolite (glucose) repression, several catabolite repression resistant mutants were selected from newly screened Bacillus firmus var. alkalophilus H609, after NTG (N-methyl-N -nitro-N-nitrosoguanidine) treatment, using 2-deoxyglucose as a nonmetabolizable analog of catabolite glucose and as a selection marker. Five catabolite repression resistant mutants were selected from about 30, 000 2-deoxyglucose resistant colonies. Relative catabolite repression indices of the selected mutants were in the range of 8~80% assuming 100% for parent strain. The amount of CGTase produced by the mutant strain CR41, which was 250 units/ml, was three times larger than that produced by its parent strain. The mutation seems to have occurred in the regulatory region of CGTase gene and not in the structural region or the glucose transporting system in cell membrane. The enzymatic properties of CGTase excreted from parent and mutant strains were also compared.

• Journal of Microbiology
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• v.34 no.1
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• pp.30-36
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• 1996

We have exmained the re-establishment of HIMRE mediated silencing function on the transcriptional activity of yeast heast shock gene HSP82. To test whether the onset of SIR repression can occur in growing cells in the rpesence of a potent inhibitor of DNA replication, HMRa/HSP82 strains with SIR4- and SIR4S$^{+}$ genetic backgrounds were arrested in S phase by incubation of a culture in 200 mM hydroxyurea for 120 min. It was clear that following a 20 minute heat shock, silencing of the HMRa/HSP82 allele in cells pretreated with hydroxyurea does occur in a SIR4-dependen fashion, even though the kinetics of repression appears to be substantially delayed. We also have tested whether re- establishement of silencing at the HMR/hsp82 locus can occur in G1-arrested cells. Cell cycle arrest at G1 phase was achieved by treatment of early log a cell cultures with .alpha.-factor mating pheromone, which induces G1 arrest. The result suggests that passage through S phase (and therefore DNA replication) is nor required for re-establishing silencer-mediated repression at the HMNRa/HSP82 locus. Finally, to test whether de nono protein synthesis is required for re-establishment of silencer-mediated repression, cells were pretreated with cycloheximide (500 /.mu.g/ml) 120 min. It was apparent that inhibiting protein synthesis delays, but does not prevent, re-establishment of silencer-mediated repression. Altogether, these results indicate that re-establishment of silencer-mediated repression is not dependent on the DNA replication and has no requirement for protein synthesis.s.

• Animal cells and systems
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• v.1 no.4
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• pp.647-651
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• 1997

We have used a transient expression assay employing Drosophila S2 cells to study the transcriptional repression activity of a 27 amino acid residue-long repression domain FS1 which was generated by a frame-shift in a pair-rule gene, even-skipped of Drosophila melanogaster. In an attempt to define a minimal requirement for the repression activity, we constructed a series of truncation mutant forms of the FS1, fused to a heterologous GAL4 DNA-binding domain, and measured their activities. All of the mutant forms, including the GAL4-FS1 (5-23) which retains the smallest number (19) of amino acid residues of FS1, were found to repress an initiator, a minimal TATA-lacking promoter, in a GAL4-binding-site-dependent manner. These findings suggest that a 19 amino acid residue-long region, rich in proline and leucine residues, is a transcriptional repression domain and may interact with the general transcription machinery.

• Journal of Microbiology and Biotechnology
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• v.17 no.10
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• pp.1727-1732
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• 2007

Phenylacetic acid (PAA) is produced by many bacteria as an antifungal agent and also appears to be an environmentally toxic chemical. The object of this study was to detect PAA using Pseudomonas putida harboring a reporter plasmid that has a PAA-inducible promoter fused to a green fluorescent protein (GFP) gene. Pseudomonas putida KT2440 was used to construct a green fluorescent protein-based reporter fusion using the paaA promoter region to detect the presence of PAA. The reporter strain exhibited a high level of gfp expression in minimal medium containing PAA; however, the level of GFP expression diminished when glucose was added to the medium, whereas other carbon sources, such as succinate and pyruvate, showed no catabolic repression. Interestingly, overexpression of a paaF gene encoding PAA-CoA ligase minimized catabolic repression. The reporter strain could also successfully detect PAA produced by other PAA-producing bacteria. This GFP-based bioreporter provides a useful tool for detecting bacteria producing PAA.