• Animal cells and systems
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• v.2 no.2
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• pp.287-295
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• 1998

The Saccharomyces cerevisiae MGMT gene encodes a O6-methylguanine DNA methyltransferase that protects cells from mutation or death by DNA alkylating agents. Using an in vitro transcription system, we analyzed its promoter region to find regulatory elements for transcription initiation. DNase I footprinting and a transcription assay showed that a functional TATA box, 5'-TGATATAGCA-3', is located in the region spanning from -25 to -34. We also found one upstream repressing sequence (URS), -333 to -213, by promoter deletion and competition analysis. Gel mobility shift assays and Southwestern blot analysis using URS region indicate specific complex formations. These results indicate that several cis-acting and trans-acting elements might be involved in the transcriptional regulation of the S. cerevisiae MGMT gene.

• Journal of Photoscience
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• v.5 no.4
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• pp.149-152
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• 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.

• The Plant Pathology Journal
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• v.17 no.3
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• pp.115-122
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• 2001

Potato virus X (PVX) is a flexuous rod-shaped virus containing a single plus-strand RNA. Viral RNA synthesis is precisely regulated by regulatory viral sequences and by viral and/or host proteins. RNA sequence element as well as stable RNA stem-loop structure in the 5' end of the genome affect accumulation of genomic RNA and subgenomic RNA (sgRNA). The putative sgRNA promoter regions upstream of the PVX triple gene block (TB) and coat protein (CP) gene were critical for both TB and CP sgRNA accumulation. Mutations that disrupted complementarity between a region at the 5' end of the genomic RNA and the sequences located upstream of each sgRNA initiation site is important for PVX RNA accumulation. Compensatory mutations that restore complementarity restored sgRNA accumulation levels. However, the extent of reductions in RNA levels did not directly correlate with the degree of complementarity, suggesting that the sequences of these elements are also important. Gel-retardation assays showed that the 5' end of the positive-strand RNA formed an RNA-protein complex with cellular proteins, suggesting possible involvement of cellular proteins for PVX replication. Future studies on cellular protein binding to the PVX RNA and their role in virus replication will bring a fresh understanding of PVX RNA replication.

• BMB Reports
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• v.56 no.3
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• pp.153-159
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• 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.

• BMB Reports
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• v.38 no.4
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• pp.500-506
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• 2005

HOX11 encodes a homeodomain-containing transcription factor which directs the development of the spleen during embryogenesis. While HOX11 expression is normally silenced through an unknown mechanism in all tissues by adulthood, the deregulation of HOX11 expression is associated with leukemia, such as T-cell acute lymphoblastic leukemia. The elucidation of regulatory elements contributing to the molecular mechanism underlying the regulation of HOX11 gene expression is of great importance. Previous reports of HOX11 regulatory elements mainly focused on the 5'-flanking region of HOX11 on the chromosome related to transcriptional control. To expand the search of putative cis-elements involved in HOX11 regulation at the post-transcriptional level, we analyzed HOX11 mRNA 3'-untranslated region (3'UTR) and found an AU-rich region. To characterize this AU-rich region, in vitro analysis of HOX11 mRNA 3'UTR was performed with human RNA-binding protein HuR, which interacts with AU-rich element (ARE) existing in the 3'UTR of many growth factors' and cytokines' mRNAs. Our results showed that the HOX11 mRNA 3'UTR can specifically bind with human HuR protein in vitro. This specific binding could be competed effectively by typical ARE containing RNA. After the deletion of the AU-rich region present in the HOX11 mRNA 3'UTR, the interaction of HOX11 mRNA 3'UTR with HuR protein was abolished. These findings suggest that HOX11 mRNA 3'UTR contains cis-acting element which shares similarity in the action pattern with RE-HuR interactions and may involve in the post-transcriptional regulation of the HOX11 gene.

• Animal cells and systems
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• v.15 no.3
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• pp.227-233
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• 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.

• Tuberculosis and Respiratory Diseases
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• v.48 no.6
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• pp.879-886
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• 2000

Background : Thyroid Transcription Factor-1(TTF-1) acts as a tissue specific transcription factor in the regulation of lung specific gene expression and as morphogenic protein during lung organogenesis. Currently, there is very little information on the cis-acting sequences and transcription factors that direct the TTF-1 gene expression. DNAse 1 hypersensitive (DH) sites represent a marker for active or potentially active chromatin and are likely to be especially important in gene regulation, being associated with many DNA sequences that regulate gene expression. It is clear that DH regions correlate with genetic regulatory loci and binding for sequence-specific DNA-binding proteins. Methods : We have used DH site assays to identify putative distal regulatory elements in H441 lung adenocarcinoma cells, which express the TTF-1 gene and HeLa cells. Results : There are four DH sites 5' of the TTF-1 gene. These sites are located at base pair approximately +150, -450, -800, and -1500 from the start of transcription. Conclusion : These data suggest that there may be at least one intragenic site and regulatory region 5' prime to the promotor region.

• BMB Reports
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• v.38 no.4
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• pp.457-467
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• 2005

Open reading frame (ORF) 3 on the Choristoneura fumiferana granulovirus (ChfuGV), located in the 11 kb fragment of the BamHI genomic bank encodes a predicted 32-kDa putative kinase protein. Bioinformatics analysis on the predicted amino acid sequence of ChfuGV PK-1 revealed the existence of 11 catalytic subdomains. Sequence analysis within the 5'-untranslated region (5'-UTR) of ChfuGV pk-1 indicates the presence of both putative early and late promoter motifs, indicating that pk-1 may be expressed throughout the infection cycle. Promoter sequence analysis reveals that pk-1 is deprived of a TATA box and appears instead to be regulated by other cis-acting transcriptional regulatory elements. Temporal transcription analysis by RT-PCR confirms the appearance of transcripts detected from 2 h p.i. until 72 h p.i. Northern blot hybridization characterizes pk-1 transcription as a 1.2 kb transcript. Homology comparisons reveal that ChfuGV PK-1 protein is most closely related to Phthorimaea operculalla granulovirus (PoGV) with 80% amino acid identity.

• Genomics & Informatics
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• v.21 no.3
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• pp.36.1-36.19
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• 2023

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

• Molecules and Cells
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• v.26 no.5
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• pp.496-502
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• 2008

Cryparin, encoded as a single copy gene (Crp) of the chestnut blight fungus Cryphonectria parasitica, is the most abundant protein produced by this fungus. However, its accumulation is decreased remarkably in C. parastica strains containing the double-stranded (ds) RNA virus Cryphonectria hypovirus 1. To characterize the transcriptional regulatory element(s) for strong expression and viral regulation, promoter analysis was conducted. Serial deletion of the Crp promoter region resulted in a step-wise decrease in promoter activity, indicating a localized distribution of genetic elements in the cryparin promoter. Promoter analysis indicated two positive and a repressive cis-acting elements. Among them, the promoter region between nt -1,282 and -907 appeared to be necessary for hypoviral-mediated down-regulation. An electrophoretic mobility shift assay (EMSA) on the corresponding promoter region (-1,282/-907) indicated two regions at (-1,257/-1,158) and (-1,107/-1,008) with the characteristic AGGAGGA-N42-GAGAGGA and its inverted repeat TCCTCTC-N54-TCCTCCT, respectively, appeared to be specific binding sites for cellular factors.