• Animal cells and systems
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• v.3 no.4
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• pp.413-415
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• 1999

Our previous report demonstrated that the rhp51$^＋$, a recA and RAD51 homolog of the fission yeast, encodes three transcripts of 1.9, 1.6 and 1.3 kb which have at least six polyadenylation sites. The 3'-end of the gene alone can direct the formation of multiple, discrete 3'ends of the transcripts. To identify the regulatory element required for the 3'-end formation of -rhp51$^＋$ deletion mapping analysis was performed. Northern blot analysis revealed that the 254-bp DNA fragment including 4 distinct poly (A) sites downstream from the Hindlll site, is crucial for normal 3'-end formation. Deletion of the 3'-terminal AU rich region caused appearance of read-through RNA, leading to enhancement of survival rate of the rhp51 deletion mutant in response to DNA damaging agent, methylmethane sulfonate (MMS). The results imply that the rhp51$^＋$ system may be useful for molecular analysis of the 3'-end formation of RNA in the fission yeast.

• Journal of Microbiology and Biotechnology
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• v.9 no.4
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• pp.488-497
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• 1999

Probing Streptomyces albus ATCC 21838 chromosomal DNA with a proline tRNA sequence resulted in an isolation of a putative integrating element in the 6.4-kb EcoRI fragment. It was found that Streptomyces lividans TK-24 transformed with a cloned DNA fragment on a multicopy plasmid, produced a higher level of spore pigment and mycelial red pigment on a regeneration agar. Furthermore, the transformant S. lividans TK-24 produced a markedly increased level of undecylprodigiosin in a broth culture. A nucleotide sequence analysis of the cloned region revealed several open reading frames homologous to the integrases of integrating plasmids or temperate bacteriophages, signal-transducing regulatory proteins with a conserved ATP-binding domain, oxidoreductases ($\beta$-ketoacyl reductase), and an AraC-like transcriptional regulator. To examine the effect on antibiotic production, each coding region was overexpressed separately from the other genes in the region in S. lividans TK-24 with; pJHS3044 for the expression of the signal-transducing regulatory protein homologue, pJHS3045 for the homologue of oxidoreductase, and pJHS3051 for the homologue of the AraC-like transcriptional regulator. Phenotypic studies of S. lividans TK-24 strains harboring plasmids for the overexpression of individual genes suggested the following effects of the genes on antibiotic production: The oxidoreductase homologue stimulated the production of actinorhodin and undecylprodigiosin, which was influenced by the culture conditions; the homologue of the AraC-like transcriptional regulator was the most effective factor in antibiotic production within all the culture conditions tested; the signal-transducing regulatory protein homologue repressed the effect due to the homologue of the AraC-like transcriptional regulator, however, the antibiotic production was derepressed upon entering the stationary phase.

• Development and Reproduction
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• v.26 no.2
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• pp.49-58
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• 2022

The differentiation and development of preadipocyte into mature adipocyte are regulated by transcription factors, such as CCAAT enhancer binding protein (Cebp) gene family and sterol regulatory element binding transcription factor 1 (Srebp1). Steroid hormones give influences on the development and function of adipocyte. The present research examined expression patterns of CCAAT enhancer binding protein alpha (Cebpa), CCAAT enhancer binding protein beta (Cebpb), CCAAT enhancer binding protein gamma (Cebpg), sterol regulatory element binding transcription factor 1 (Srebp1), androgen receptor (Ar), and estrogen receptors (Esr) among different epididymal fat parts during postnatal period by quantitative real-time polymerase chain reaction. In the distal epididymal fat, expression of Cebpa, Cebpb, Cebpg, Srebp1, Ar, and Esr2 was increased until 12 months of age, while expression of Esr1 was decreased at 5 months of age and was not detectable after 8 months of age. In the proximal epididymal fat, transcript levels of Cebps and Srebp1 were increased at 8 months of age, followed by decreases of Cebpb and Cebpg transcript levels at 12 months of age. An additional increase of Srebp1 expression was observed at 12 months of age. Expression of Ar and Esr2 were increased until 8 months of age, followed by a drop of Ar expression level at 12 months of age. Expression pattern of Esr1 was similar to that in the distal epididymal fat. In the tail epididymal fat, expression of Cebpa, Cebpg, Srebp1, Ar, and Esr2 was increased with age. Esr1 was not detectable at all. The highest level of Cebpb was observed at 8 months of age. These data suggest the possibility of developmental and functional differentiation among the epididymal fat parts.

• BMB Reports
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• v.42 no.12
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.11
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• pp.1628-1633
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• 2001

A goat ${\beta}$-casein gene was cloned and sequenced. Our previous study had determined the nucleotide sequences of the 5' flanking region and the structural gene including all 9 exons. In the present study, investigations were done on the regulatory sequences in the 5' flanking region of the goat ${\beta}$-casein gene by aligning and comparing it with the same gene from other mammals. The results showed that -200/-1 bp of the 5' flanking sequences contained six conserved clusters, in which the sites of gene expression regulated by the transcription factor and hormone might exist. It showed that fourteen glucocorticoid receptor elements, two cAMP responsive elements, two SV40 virus enhancer core sequences, two OCT-1 binding elements and one CTF/NF-1 binding element were dispersed in the 5' flanking region of goat ${\beta}$-casein gene. Our findings are perhaps valuable for the elucidation of the molecular mechanisms that control the expression of the goat ${\beta}$-casein gene.

• Journal of Applied Biological Chemistry
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• v.42 no.2
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• pp.62-65
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• 1999

Iron regulatory proteins (IRPs) 1 and 2 bind with equally high affinity to specific RNA stem-loop sequences known as iron-responsive elements (IRE) which mediate the post-transcriptional regulation of many genes of iron metabolism. To study putative IRE-like sequences in RNA transcripts using the IRP-IRE interaction, Eight known genes from database were selected and the RNA binding activity of IRE-like sequences were compared to IRP-2. Among them, the IRE-like sequence in 3'-untranslational region (UTR) of divalent ration transporter-1 (DCT-1) shows a significant RNA binding affinity. This finding predicts that IRE consensus sequence present within 3'-UTR of DCT-1 might confer the regulation by IRP-2.

• Genomics & Informatics
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• v.19 no.1
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• pp.3.1-3.12
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• 2021

Functional interpretation of noncoding genetic variants associated with complex human diseases and traits remains a challenge. In an effort to enhance our understanding of common germline variants associated with lung cancer, we categorize regulatory elements based on eight major cell types of human lung tissue. Our results show that 21.68% of lung cancer-associated risk variants are linked to noncoding regulatory elements, nearly half of which are cell type-specific. Integrative analysis of high-resolution long-range chromatin interactome maps and single-cell RNA-sequencing data of lung tumors uncovers number of putative target genes of these variants and functionally relevant cell types, which display a potential biological link to cancer susceptibility. The present study greatly expands the scope of functional annotation of lung cancer-associated genetic risk factors and dictates probable cell types involved in lung carcinogenesis.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1997.04a
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• pp.81-81
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• 1997

We previously demonstrated an enhancer-like positive regulatory element within a 259-bp sequence (-2352 to-2094 bp) of the human CYP1A2 gene in HepG2 cells. Three protein binding sites were identified by DNase I footprint analyses within the 259-bp sequence: protected region A PRA ( -2283 to-2243 bp), PRB (-2218 to-2187 bp), and PRC (-2124 to-2098 bp) (I. Chung and E. Bresnick, Mol. Pharmacol. 47, 677-685, 1995). In the present study, the functional significance of those protected regions was examined. Transfection experiments with deletion and substitution mutants defined the PRB and PRC as containing positive and negative regulatory elements, respectively. Human breast carcinoma MCF-7 cells were cotransfected with a hepatocyte nuclear factor-1 (HNF-1) expression vector and CYP1A2 promoter-or thymidine kinase promoter-luciferase remoter gene constructs. HNF-1, which contributes to the liver specificity of genes, enhanced reporter gene activity in a PRC sequence-dependent manner. These results suggested that PRC could exist bound to a repressor which was displaceable by other transcription factors such as HNF-1. Results obtained by transfection of HepG2 hepatoma cells with various PRB substitution mutant-luciferase gene fusion constructs indicated that the entire sequence of PRB was necessary for promoter activity. Consequently, the regulation of CYP1A3 expression is very complex, requiring a number of both positive and negative regulatory factors.

• Molecules and Cells
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• v.43 no.4
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• pp.331-339
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• 2020

Genetic modifications in noncoding regulatory regions are likely critical to human evolution. Human-accelerated noncoding elements are highly conserved noncoding regions among vertebrates but have large differences across humans, which implies human-specific regulatory potential. In this study, we found that human-accelerated noncoding elements were frequently coupled with DNase I hypersensitive sites (DHSs), together with monomethylated and trimethylated histone H3 lysine 4, which are active regulatory markers. This coupling was particularly pronounced in fetal brains relative to adult brains, non-brain fetal tissues, and embryonic stem cells. However, fetal brain DHSs were also specifically enriched in deeply conserved sequences, implying coexistence of universal maintenance and human-specific fitness in human brain development. We assessed whether this coexisting pattern was a general one by quantitatively measuring evolutionary rates of DHSs. As a result, fetal brain DHSs showed a mixed but distinct signature of regional conservation and outlier point acceleration as compared to other DHSs. This finding suggests that brain developmental sequences are selectively constrained in general, whereas specific nucleotides are under positive selection or constraint relaxation simultaneously. Hence, we hypothesize that human- or primate-specific changes to universally conserved regulatory codes of brain development may drive the accelerated, and most likely adaptive, evolution of the regulatory network of the human brain.

• Fisheries and Aquatic Sciences
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• v.12 no.2
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• pp.98-103
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• 2009

The potential utility of the rockbream (Oplegnathus fasciatus) $\beta$-actin 5'-upstream sequence as a regulatory element for DNA vaccination was evaluated based on in vitro and in vivo heterologous expression assays. In the in vitro transfection experiment, the efficacy of the rockbream $\beta$-actin promoter to drive the expression of a downstream lacZ gene was significantly higher (more than fourfold) than that of the human cytomegalovirus (hCMV) promoter in two fish cell lines (grunt Haemulon plumierii fin and bluegill Lepomis macrochirus fry cell lines). In contrast, the functional activity of the rockbream $\beta$-actin promoter was hardly detectable in a mammalian mouse embryonic fibroblast cell line. Rockbream skeletal muscles injected in vivo with a GFP reporter construct driven by the $\beta$-actin promoter displayed the significantly higher expression of a GFP protein (more than threefold) than did those injected with hCMV promoter driven construct. Data from this study suggest that the homologous rockbream $\beta$-actin promoter could be used as a potential regulator for DNA vaccination in this species.