• Asian-Australasian Journal of Animal Sciences
• /
• v.14 no.11
• /
• pp.1628-1633
• /
• 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
• /
• v.42 no.2
• /
• pp.62-65
• /
• 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.

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

• Applied Biological Chemistry
• /
• v.38 no.5
• /
• pp.387-392
• /
• 1995

To study the regulatory expression mechanism of soybean glycinin gone, Gy2, the 5' upstream region of the gene was searched for the presence of putative regulatory elements by nucleotide sequencing. It revealed various kinds of regulatory sequence elements commonly found in plant storage protein genes. There were canonical promoter sequences, TATA box (TATAAT) and AGGA box (GAAT) which are common in the 5' upstream region of the plant genes. The embryo factor binding sequence, RY repeat, CACA sequences, ${\alpha}$-conglycinin enhancer-like sequences were also found. To delineate the function of these sequences, 5' upstream deletion mutants of Gy2 were prepared and fused to the ${\alpha}$-glucuronidase (GUS) gene. Each chimeric construct was transferred into soybean protoplasts for transient assay, which led to the identification of the sequences between -281 and -223, -170 and -122, of Gy2 promoter as negative regulatory elements, and the sequences between -223 and -170, -122 and -16 as positive regulatory elements. These results are consistent in transformed tobacco plants as well. The serially deleted promoter fragments fused to the GUS were transformed into Nicotiana tabacum by Agrobacterium tumefaciens using the binary vector system. GUS activity of Gy2 promoter deletion constructs was detected only in seeds but not in leaves with different levels of expression as in transient assay. These results suggest that the glycinin Gy2 promoter drives a tissue-specific expression in transgenic tobacco plants.

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

• Proceedings of the Zoological Society Korea Conference
• /
• 1995.10b
• /
• pp.76-76
• /
• 1995

No Abstract, See Full Text

• Journal of Plant Biotechnology
• /
• v.33 no.4
• /
• pp.233-236
• /
• 2006

Human serum albumin (HSA) is the most abundant protein in plasma and is the most often used intravenous protein in many human therapies. However, HSA is currently extracted only from plasma because commercially feasible recombinant expression systems are not available. This study attempted to develop an efficient system for recombinant HSA production by chloroplast transformation of tobacco. A HSA cDNA was isolated from a cDNA library constructed with human liver tissue. Chloroplast transformation vectors were constructed by introducing various regulatory elements to HSA regulatory sequences. Vectors were delivered by particle bombardment into leaf explants and chloroplast-transformed plants were subsequently regenerated into whole plants. Southern blot analysis confirmed that the HSA cDNA was incorporated between rps12 and orf70B of the chloroplast genome as designed. Western blot analysis revealed that hyper-expression and increasing the stability of HSA were achieved by modification of the regulatory sequences using the psbA5'UTRs in combination with elements of the 14 N-terminal amino acids of the GFP and the FLAG tag. However, only plants transformed with the vector containing all of these elements were able to accumulate HSA.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.7
• /
• pp.3329-3334
• /
• 2016

Cancer is thought to be a direct result of transcriptional misregulation. Broad analysis of transcriptional regulatory elements in healthy and cancer cells is needed to understand cancer development. Nucleases regulatory domains are recruited to bind and manipulate a specific genomic locus with high efficacy and specificity. TALENs (transcription activator-like effector nuclease) fused to endonuclease FokI have been used widely to target specific sequences to edit several genes in healthy and cancer cells. This approach is promising to target specific cancer genes and for this purpose it is needed to pack such TALENs into viral vectors. There are some considerations which control the success of this approach, targeting appropriate sequences with efficient construction of TALENs being crucial factors. We face some obstacles in construction of TALENs; in this study we made a modification to the method of Cermk et al 2011 and added one step to make it easier and increase the availability of constructs.

• Proceedings of the Zoological Society Korea Conference
• /
• 2003.08a
• /
• pp.169.1-169
• /
• 2003

No Abstract, See Full Text

• Genomics & Informatics
• /
• v.5 no.4
• /
• pp.143-151
• /
• 2007

To understand the mechanism of transcriptional regulation, it is essential to detect promoters and regulatory elements. Various kinds of methods have been introduced to improve the prediction accuracy of regulatory elements. Since there are few experimentally validated regulatory elements, previous studies have used criteria based solely on the level of scores over background sequences. However, selecting the detection criteria for different prediction methods is not feasible. Here, we studied the calibration of thresholds to improve regulatory element prediction. We predicted a regulatory element using MATCH, which is a powerful tool for transcription factor binding site (TFBS) detection. To increase the prediction accuracy, we used a regulatory potential (RP) score measuring the similarity of patterns in alignments to those in known regulatory regions. Next, we calibrated the thresholds to find relevant scores, increasing the true positives while decreasing possible false positives. By applying various thresholds, we compared predicted regulatory elements with validated regulatory elements from the Open Regulatory Annotation (ORegAnno) database. The predicted regulators by the selected threshold were validated through enrichment analysis of muscle-specific gene sets from the Tissue-Specific Transcripts and Genes (T-STAG) database. We found 14 known muscle-specific regulators with a less than a 5% false discovery rate (FDR) in a single TFBS analysis, as well as known transcription factor combinations in our combinatorial TFBS analysis.