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Gang Zhao,Chunzheng Gao,Dayong Peng,Meng Chen,Guilai Zuo,Shiying Shan 한국유전학회 2016 Genes & Genomics Vol.38 No.7
Spinal cord injury (SCI) remains to be the most devastating type of trauma for patients because of long lasting disability and limited response to the acute drug administration and efforts at rehabilitation. With the purpose to identify potential targets for SCI treatment and to gain more insights into the mechanisms of SCI, the microarray data of GSE2270, including 119 raphe magnus (RM) samples and 125 sensorimotor cortex (SMTC) samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened inRM group and SMTC group compared with their corresponding controls, respectively. A protein–protein interaction (PPI) network was constructed based on the common DEGs identified in both RM group and SMTC group. Gene ontology (GO) and pathway enrichment analyses of the overlapping DEGs were performed. Furthermore, the common DEGs enriched in each pathway were analyzed to identify significant regulatory elements. Totally, 173 overlapping DEGs (130 up-regulated and 43 down-regulated) were identified in both RM and SMTC samples. These overlapping DEGs were enriched in different GO terms. Pathway enrichment analysis revealed that DEGs were mainly related to inflammation and immunity. CD68 molecule (CD68) was a hub protein in the PPI network. Moreover, the regulatory network showed that ras-related C3 botulinum toxin substrate 2 (RAC2), CD44 molecule (CD44), and actin related protein 2/3 complex (ARPC1B) were hub genes. RAC2, CD44, and ARPC1B may be significantly involved in the pathogenesis of SCI by participating significant pathways such as extracellular matrix-receptor signaling pathway and Toll-like receptor signaling pathway.
Yujie Zhang,Xu Zhang,Nini Cheng,Yanping Li,Jinyi Xing 한국유전학회 2015 Genes & Genomics Vol.37 No.7
Identification of essential fragments in the promoter region of genes to drive tissue-specific expression of exogenous genes in the skeletal muscle is obligatory for animal transgenic study. The skeletal a-actin is a major protein of the thin filaments of skeletal muscle fiber. In this study, the specificity and activity of porcine skeletal aactin gene promoter were investigated by approaches of cell transfection and assayed with green fluorescent protein (GFP) and dual luciferase reporter activity, respectively. The results revealed that the obtained 3717 bp fragment of porcine skeletal a-actin gene promoter drives GFP to be expressed uniquely in murine C2C12 cells, and two segments of 2.0–2.3 and 0.06–0.37 kb in the promoter region were essential for porcine skeletal a-actin gene expression. The regulatory elements in the 0.06–0.37 kb fragment were further investigated, and when it is deleted or the CArG box within this fragment was mutated, the promoter activity was reduced to 20 or 43 % (P\0.01), respectively, compared to the 3.04 kb segment, suggesting an important role of CArG box in regulating porcine skeletal a-actin gene transcription. The results may provide reference for creating transgenic pigs to express exogenous genes uniquely in pork.
So Yun Park,Yong Tae Park,Kyoon Eon Kim,Myung Chull Rhee,조희중,Dong Sun Kim 한국분자세포생물학회 2002 Molecules and cells Vol.13 No.2
The expression of the N-type voltage-gated calcium channel α1B gene is restricted to neurons by a 5′- upstream region (-3992 to -1788) that contains negative regulatory element(s) that are active in nonneuronal cells. A 39 bp DNA element, which is repeated nine times in a head-to-tail fashion, was found within the same region. To examine whether this direct repeat (DR) may function as a negatively acting cisregulatory element, several fusion plasmids, DR- 110α1BLUC (1X), DR-SV40LUC (1X, 2X), in which one or two copies of the DR fragment were subcloned upstream of the homologous and heterologous promoters, were transiently transfected into HeLa and NS20Y cells. The promoter activity of DR-110α1BLUC (1X) decreased to approximately 17% of the 110α1BLUC construct in HeLa cells. The expression of the DRSV40LUC (1X) and DR-SV40LUC (2X) plasmids was also reduced to 50 to 23% of the levels that were observed in the pGL2-Promoter in the same cells. However, no repression of the DR constructs was observed in NS20Y cells. An electrophoretic mobility shift assay showed that two DR-specific complexes were detected in HeLa cells, but not in NS20Y cells. In addition, Southwestern blotting revealed the presence of approximately 33 and 43 kDa proteins in HeLa cells. Overall, these results suggest that a 39 bp DNA element might act as repressor in non-neuron cells through the specific interactions of the DNA-proteins.
Won Cheol Vim,Cheol Seong Jang 한국육종학회 2007 한국육종학회지 Vol.39 No.4
In order to uncover gene regulatory networks clustering of co-expressing genes was performed using a rice micorarray dataset of 155 gene expression omnibus sample (GSM) plates in NCBI, generating a total of 1660 clusters. One cluster with 85 co-expressing genes was measured with the correlation coefficient between pairs, resulting in an average r value of 0.66 with a range of -0.08 to 0.98. This result might support the notion that genes included in each cluster play common functional role(s). We also retrieved 23 Affymetrix GeneChip spots IDs corresponding to each of candidate genes related to abiotic stresses obtained from the P1antQTL-GE database and subsequently detected 23 clusters including co-expressing genes with each of the genes. Expression profiles of co-expressing genes revealed some degree of tissue-specific expression patterns, probably reflecting the existence of, at least partial, parallel versions of stress-related networks with evolutionary process, such as subfuntionalization. The finding that several cis-elements related to abiotic stresses was detected by differences in frequency between co-expressing genes and randomly selected genes. Clustering, expression profiles, and putative cis-acting regulatory elements of co-expressing genes related to abiotic stresses may provide clues to shed further light on the gene regulatory network of stress-responsive pathway.
RAHMAN MD MUSTAFIZUR,Rahman Md Mizanor,엄준섭,전종성 한국식물학회 2021 Journal of Plant Biology Vol.64 No.1
Trehalose-6-phosphate phosphatase (TPP) plays a key role in trehalose metabolism in plants. Here, we performed comprehensive in silico analyses and identified 12 OsTPPs (Oryza sativa TPPs) utilizing various bioinformatics tools. Phylogenetic tree, accomplished with OsTPPs and TPPs from 11 monocot and dicot species, was divided mainly into two clades, each clade containing six OsTPPs. Exon–intron distribution was related to phylogenetic clades. All OsTPPs are distributed within nine chromosomes (chr.), except Chr. 1, Chr. 5 and Chr. 11. OsTPPs were found to be stable in nature according to the 3-D structure prediction. Cis-regulatory elements (CREs) were also analyzed using 2 kb upstream of start codon for each gene to predict their biological functions. We categorized all CREs in five distinct groups based on core elements, stress response, cellular development, hormonal regulation, and unknown function, distributed in a range of 3–14 CREs in each group. Interestingly, our expression analysis showed that OsTPPs were more upregulated in response to drought and cold stresses compared to salt stress. Abundance of stress-related CREs found signifies TPPs’ possible role in stress response, which may facilitate to find related transcription factors and unveil complex molecular mechanisms during stress response.
Sequence and functional analysis of an upstream regulatory region of human HOXA7 gene
Min, Wongi,Cho, Myungsun,Jang, Seung Ik,Chang, Hwa-Hyoung,Lee, Chul-Sang,Jun, Moo-hyung,Kim, Myoung Hee 충남대학교 생물공학연구소 1997 생물공학연구지 Vol.5 No.-
The Hox genes have been known to be involved in pattern formation during vertebrate development through differential expression along the anteroposterior body axis. Human homologue of position-specific regulatory region of murine Hoxa-7 was cloned from human genomic library. The restriction map of the 18-kb insert was determined. of which a 3.9-kb region was sequenced. Homology plot between the murine and the corresponding human sequence showed high sequence conservation over 70% in several regions. The homologous region has been reduced to about 1.1 kb (HCR: human control region), which contained several putative factor binding sites. The function of HCR was analyzed in transgenic mice and turned out to be a position-specific regulatory clement of human, setting the precise anterior boundary of expression in transgenic embryos: at day 12.5 postcoitum a distinct anterior limit of expression was noted at the level of C5 in neural tube and spinal ganglia in transgenic cmbryos. These results indicatc that the regulatory sequences as well as the molecular mechanism for Hox gene expression are highly conserved among vcrtebrates.
Ardiyanti, Astrid,Abe, Tsuyoshi,Tameoka, Nanae,Kobayashi, Eiji,Shoji, Noriaki,Ohtani, Yoshihisa,Suzuki, Keiichi,Roh, Sang-Gun,Katoh, Kazuo Asian Australasian Association of Animal Productio 2012 Animal Bioscience Vol.25 No.8
Two SNPs, i.e. L127V and T172M, of bovine growth hormone (GH) causing the presence of GH gene haplotypes A, B, and C was previously shown to alter intramuscular fatty acid (FA) composition in Japanese Black (JB) heifers. To determine the SNP effect on somatotropic hormone concentration and lipogenesis, we measured plasma GH, insulin, and insulin-like growth factor-1 (IGF-1) concentrations. We also measured mRNA levels of fatty acid synthase (FASN), stearoyl-coA desaturase (SCD), and sterol regulatory element binding proteins-1 (SREBP-1) and FA composition in diaphragm tissues. Heifers with genotype CC had the lowest plasma insulin concentration and FASN and SCD mRNA levels among genotypes. FASN mRNA levels in haplotype A tended to positively correlate with saturated FA (SFA) content and negatively correlated with C18:2 and unsaturated FA (USFA) contents. SCD mRNA levels in haplotype A positively correlated with monounsaturated FA (MUFA) contents and negatively correlated with C18:0 content. They also tended to positively correlate with C16:1, C18:1, and USFA contents and USFA/SFA ratio and negatively correlate with SFA content. Taken together, GH gene polymorphism affects the lipogenic genes expression levels and their relationships with fatty acid compositions in diaphragm tissues of JB heifers at 31 months of age.