• BMB Reports
• /
• 제42권12호
• /
• pp.823-828
• /
• 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.

• Journal of Photoscience
• /
• 제5권4호
• /
• pp.149-152
• /
• 1998

Expression of light-harvesting chlorophyll a/b-binding protein gene(cab) is repressed in the dark and activited by light. However, the detail of its regulatory mechanism is not characterized so far. To identify the interactions of cis-acting elements and trans-acting factors involvedin this regulation, nuclear extracts from the light-grown and dark-adapted Arabidopsis thaliana leaves were anlayzed for mobility shift assay against 134bp fragments had two retarded bands and one retardation band, respectively, both in light-grown and dark-adapted bands in the dark-adapted tissues. A new retardation the cab 3 expression in the dark. Several light regulatory motifs are scattered in the 146 bp region of cab 3 promoter. One of the light-regulatory motifs could be the binding site for the negative regulatory factor.

• Natural Product Sciences
• /
• 제10권5호
• /
• pp.197-206
• /
• 2004

Cytochrome P4501A2 (CYP1A2) is responsible for the metabolic activation of a number of aromatic amines and amides to mutagenic and carcinogenic moieties. Considerable variations in the level of CYP1A2 expression in humans have been reported. Thus, the level of human CYP1A2 may determine an individuals susceptibility to these chemicals. Given its importance, the molecular mechanisms of CYP1A2 regulation have been studied by many groups. Direct interactions between transcription factors with the promoters of the gene represent one of the primary means by which the expression of CYP1A2 is controlled. In this review, several important cis elements, transcription factors and the effects of deacetylation/methylation of promoter regions that play an important role in the induction by PAHs as well as constitutive expression of human CYP1A2 are discussed.

• 한국정밀공학회:학술대회논문집
• /
• 한국정밀공학회 1997년도 춘계학술대회 논문집
• /
• pp.703-707
• /
• 1997

DUe to the requirement of high precision and the complexity during the tool design for electron gun elements, it sometimes causes human-errors. Also, in the case of beginners, they have more trial and error than skilled engineers. To remove these problems and increase the productivity in the practice field, it need the deveiopment of CAD system for electron gun element tools. Through this study, a CAD system of electron gun element tools which is used by used by knowledge base system including expert's technology in the practics, has been developed. To developed this system, it has used C-language under HP-UNIX system and CIS customer language of the EXCESS CAD/CAM system. An application of this system will provide effective aids to the designer in this field.

• 한국정밀공학회지
• /
• 제15권10호
• /
• pp.27-33
• /
• 1998

Due to the requirement of high precision and complexity during the die design for electron gun elements, it sometimes causes human-errors. In addition, in the case of beginners, they have more trial and error than skilled engineers. To remove these problems and increase the productivity in the practice field, it needs the development of CAD system for electron gun element progressive die. Through this study, a CAD system of electron gun element progressive die, which is used, by knowledge base system including expert's technology in the practice, has been developed. To develop this system, it has used C-language under HP-UNIX system and CIS customer language of the EXCESS CAD/CAM system. An application of this system will provide effective aids to the designer in this field.

• BMB Reports
• /
• 제54권5호
• /
• pp.233-245
• /
• 2021

In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.

• Genomics & Informatics
• /
• 제5권4호
• /
• pp.174-178
• /
• 2007

The earliest stages of mammalian embryogenesis are governed by the activity of maternally inherited transcripts and proteins. Cytoplasmic polyadenylation of selected maternal mRNA has been reported to be a major control mechanism of delayed translation during preimplantation embryogenesis in mice. The presence of cis-elements required for cytoplasmic polyadenylation (e.g., CPE) can serve as a useful tag in the screening of maternal genes partaking in key functions in the transcriptionally dormant egg and early embryo. However, due to its relative simplicity, UA-rich sequences satisfying the canonical rule of known CPE consensus sequences are often found in the 3'-UTR of maternal transcripts that do not actually undergo cytoplasmic polyadenylation. In this study, we developed a method to confirm the validity of candidate CPE sequences in a given gene by a multiplex comparison of 3'-UTR sequences between mammalian homologs. We found that genes undergoing cytoplasmic polyadenylation tend to create a conserved block around the CPE, while CPE-like sequences in the 3'-UTR of genes lacking cytoplasmic polyadenylation do not exhibit such conservation between species. Through this cross-species comparison, we also identified an alternative CPE in the 3'-UTR of tissue-type plasminogen activator (tPA), which is more likely to serve as a functional element. We suggest that verification of CPEs based on sequence conservation can provide a convenient tool for mass screening of factors governing the earliest processes of mammalian embryogenesis.

• 한국산림과학회지
• /
• 제88권4호
• /
• pp.562-567
• /
• 1999

채취시기에 따른 황칠나무 잎중의 화학성분의 변화를 분석한 결과 수분 함량은 계절이 지남에 따라 점점 감소하였으나 지방, 회분 및 섬유 함량은 오히려 점점 증가하였고 단백질 함량은 봄부터 여름까지는 감소하다가 가을에서 겨울로 감에 따라 다시 증가하는 경향을 보였다. 유리당은 검출된 세 종류의 당이 모두 봄으로부터 겨울로 감에 따라 점정 증가하는 것으로 나타났고 지방산은 일반적으로 포화지방산보다 불포화지방산이 더 많이 함유되어 있었으며, 가장 많이 함유된 포화지방산 및 불포화지방산은 계절에 관계없이 각각 arachidic acid 및 cis-13,16-docosadienoic acid였다. 유리 아미노산은 15종이 검출되었는데 계절에 관계없이 arginine의 함량이 가장 높았고 계절이 지남에 따라 점차 감소하는 것으로 나타났다. 무기성분은 채취시기에 따라 그 함량이 약간씩 차이가 있어서 칼슘 또는 칼륨이 가장 많이 함유되어 있었고 다른 무기성분의 함량은 거의 동일한 경향을 보였다. 총 비타민 C 함량은 계절이 점차 겨울로 감에 따라 감소하는 경향이었으나 수용성 탄닌 함량은 오히려 증가하는 경향을 보여 새잎보다 성숙된 겨울에 채취한 잎에 훨씬 더 높은 것으로 밝혀졌다.

• BMB Reports
• /
• 제56권3호
• /
• pp.153-159
• /
• 2023

Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between trans-acting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cis-regulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes.

• Animal cells and systems
• /
• 제15권3호
• /
• pp.227-233
• /
• 2011

The Nramp1/Slc11a1 locus encodes a proton-coupled divalent cation transporter, expressed in late endosomes/lysosomes of macrophages, that constitutes a component of the innate immune response to combat intracellular pathogens and it was shown to play an important role in regulating inherent immunity. The previously identified Z-DNA forming polymorphic repeat(GT)n in the promoter region of the human Nramp1 gene does act as a functional polymorphism influencing gene expression. Research has shown that INF-${\gamma}$, TNF-${\alpha}$, IL-$1{\beta}$ and bacteria LPS increase the level of Nramp1 expression. However, the molecular mechanism for Nramp1 gene regulation is unclear. In this research, bovine Nramp1 5'-flanking region (-1748~+769) was cloned and analyzed by bioinformatics. Then to find the core promoter and the cis-acting elements, deletion analysis of promoter was performed using a set of luciferase reporter gene constructs containing successive deletions of the bovine Nramp1 5'-flanking regions. Promoter activity analysis by the dual luciferase reporter assay system showed that the core promoter of Nramp1 was located at +58~-89 bp. Some positive regulatory elements are located at -89~-205 bp and -278~-1495 bp. And the repressor elements were in region -205~-278 bp, intron1 and -1495~-1748 bp. LPS-responsive regions were located at -1495~-1748 bp and -278~-205 bp. The present study provides an initial effort to explore the molecular mechanism of transcriptional activation of the bovine Nramp1 gene and should facilitate further studies to decode the complex regulatory process and for molecular breeding for disease resistance in bovines.