• Molecules and Cells
• /
• v.37 no.5
• /
• pp.357-364
• /
• 2014

Medulloblastoma, the most common malignant brain tumor in children, is a disease whose mechanisms are now beginning to be uncovered by high-throughput studies of somatic mutations, mRNA expression patterns, and epigenetic profiles of patient tumors. One emerging theme from studies that sequenced the tumor genomes of large cohorts of medulloblastoma patients is frequent mutation of RNA binding proteins. Proteins which bind multiple RNA targets can act as master regulators of gene expression at the post-transcriptional level to co-ordinate cellular processes and alter the phenotype of the cell. Identification of the target genes of RNA binding proteins may highlight essential pathways of medulloblastomagenesis that cannot be detected by study of transcriptomics alone. Furthermore, a subset of RNA binding proteins are attractive drug targets. For example, compounds that are under development as anti-viral targets due to their ability to inhibit RNA helicases could also be tested in novel approaches to medulloblastoma therapy by targeting key RNA binding proteins. In this review, we discuss a number of RNA binding proteins, including Musashi1 (MSI1), DEAD (Asp-Glu-Ala-Asp) box helicase 3 X-linked (DDX3X), DDX31, and cell division cycle and apoptosis regulator 1 (CCAR1), which play potentially critical roles in the growth and/or maintenance of medulloblastoma.

• Animal Bioscience
• /
• v.37 no.4
• /
• pp.567-575
• /
• 2024

Objective: This study aimed to identify genes regulated by cyclin dependent kinases 5 (CDK5) that participate in hair pigmentation in mice. Methods: The mRNA expression profiles of skin samples from CDK5-knockdown mice were constructed using high-throughput RNA sequencing and compared with those of wild-type mice. Results: In total, 8,002 known genes were differentially expressed between CDK5-knockdown and wild-type mice. Of these, 3,658 were upregulated and 4,344 were downregulated in the skin of CDK5-knockdown mice. An additional 318 previously unknown genes were also differentially expressed, with 171 downregulated and 147 upregulated genes in the skin of CDK5-knockdown mice. Of the known genes expressed in mouse skin, 80 were associated with hair color, with 61 showing lower expression and 19 exhibiting higher expression in skin of CDK5-knockdown mice. Importantly, the expression of the tyrosinase-related protein 1 (TYRP1) and the calcium signaling pathway were also found to be regulated by CDK5, suggesting that pigmentation is regulated by CDK5 via the calcium signaling pathway and TYRP1. Conclusion: The transcriptome profiles obtained from the skin of CDK5-knockdown mice compared to wild-type mice provide a valuable resource to help understand the mechanism by which CDK5 regulates melanogenesis in mice and other animals.

• Toxicological Research
• /
• v.27 no.1
• /
• pp.43-48
• /
• 2011

Even though exposure to benzene has been linked to a variety of cancers including leukemia, the detailed molecular mechanisms relevant to benzene-induced carcinogenesis remain to be clearly elucidated. In this study, we evaluated the effects of benzene on differential gene expression in a leukemia cell line. The K562 leukemia cell line used in this study was cultured for 3 h with 10 mM benzene and RNA was extracted. To analyze the gene expression profiles, a 41,000 human whole genome chip was employed for cDNA microarray analysis. We initially identified 6,562 genes whose expression was altered by benzene treatment. Among these, 3,395 genes were upregulated and 3,167 genes were downregulated by more than 2-fold, respectively. The results of functional classification showed that the identified genes were involved in biological pathways including transcription, cell proliferation, the cell cycle, and apoptosis. These gene expression profiles should provide us with further insights into the molecular mechanisms underlying benzene-induced carcinogenesis, including leukemia.

• Korean Journal of Ichthyology
• /
• v.22 no.1
• /
• pp.17-24
• /
• 2010

The present study investigated the expression of glucocorticoid receptor (GR) mRNA as a stress response during salinity changes (35, 10, and 0 psu) and water temperature changes (from $20^{\circ}C$ to $30^{\circ}C$, $1^{\circ}C$/day) in black porgy. We cloned the full-length GR cDNA from the kidney and examined its expression in the gill, kidney, and intestine by quantitative real-time PCR (QPCR) during salinity and water temperature changes. During salinity changes, the levels of GR mRNA in the gill, kidney, and intestine were highest at 0 psu, and the levels of plasma cortisol and glucose were elevated, but triiodothyronine ($T_3$) decreased. Also, during water temperature changes, the levels of GR mRNA in the gill, kidney, and intestine increased at $30^{\circ}C$. Plasma parameters also increased with an increase in water temperature. Therefore, this upregulation of GR mRNA was a good indicator of stress, such as those resulting from changes in salinity and water temperature.

• Genomics & Informatics
• /
• v.21 no.1
• /
• pp.2.1-2.14
• /
• 2023

Microglia, similar to peripheral macrophages, are the primary immune cells of the central nervous system (CNS). Microglia exist in the resting state in the healthy CNS, but can be activated and polarized into either M1 or M2 subtypes for immune defense and the maintenance of CNS homeostasis by multiple stimuli. Several long noncoding RNAs (lncRNAs) mediate human inflammatory diseases and neuropathologies by regulating their target genes. However, the function of common lncRNAs that contribute to microglial activation remains unclear. Thus, we used bioinformatic approaches to identify common lncRNAs involved in microglial activation in vitro. Our study identified several lncRNAs as common regulators of microglial activation. We identified 283 common mRNAs and 53 common lncRNAs during mouse M1 microglial activation processes, whereas 26 common mRNAs and five common lncRNAs were identified during mouse M2 microglial activation processes. A total of 648 common mRNAs and 274 common lncRNAs were identified during the activation of human M1 microglia. In addition, we identified 1,920 common co-expressed pairs in mouse M1 activation processes and 25 common co-expressed pairs in mouse M2 activation processes. Our study provides a comprehensive understanding of common lncRNA expression profiles in microglial activation processes in vitro. The list of common lncRNAs identified in this study provides novel evidence and clues regarding the molecular mechanisms underlying microglial activation.

• BMB Reports
• /
• v.53 no.5
• /
• pp.278-283
• /
• 2020

Muscle fibers are generally formed as multinucleated fibers that are differentiated from myoblasts. Several reports have identified transcription factors and proteins involved in the process of muscle differentiation, but the roles of microRNAs (miRNAs) in myogenesis remain unclear. Here, comparative analysis of the miRNA expression profiles in mouse myoblasts and gastrocnemius (GA) muscle uncovered miR-3074-3p as a novel miRNA showing markedly reduced expression in fully differentiated adult skeletal muscle. Interestingly, elevating miR-3074-3p promoted myogenesis in C2C12 cells, primary myoblasts, and HSMMs, resulting in increased mRNA expression of myogenic makers such as Myog and MyHC. Using a target prediction program, we identified Caveolin-1 (Cav1) as a target mRNA of miR-3074-3p and verified that miR-3074-3p directly interacts with the 3' untranslated region (UTR) of Cav1 mRNA. Consistent with the findings in miR-3074-3p-overexpressing myoblasts, knockdown of Cav1 promoted myogenesis in C2C12 cells and HSMMs. Taken together, our results suggest that miR-3074-3p acts a positive regulator of myogenic differentiation by targeting Cav1.

• Animal Bioscience
• /
• v.35 no.6
• /
• pp.814-825
• /
• 2022

Objective: This study was conducted to identify the functional long non-coding RNAs (lncRNAs) for swine lactation by RNA-seq data of mammary gland. Methods: According to the RNA-seq data of swine mammary gland, we screened lncRNAs, performed differential expression analysis, and confirmed the functional lncRNAs for swine lactation by validation of genome wide association study (GWAS) signals, functional annotation and weighted gene co-expression network analysis (WGCNA). Results: We totally identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition, and the expressions of most of lncRNAs were strongly changed from day -2 to day +1. Further, the GWAS signals of sow milk ability trait were significantly enriched in DE lncRNAs. Functional annotation revealed that these DE lncRNAs were mainly involved in mammary gland and lactation developing, milk composition metabolism and colostrum function. By performing weighted WGCNA, we identified 7 out of 12 lncRNA-mRNA modules that were highly associated with the mammary gland at day -14, day -2, and day +1, in which, 35 lncRNAs and 319 mRNAs were involved. Conclusion: This study suggested that 18 lncRNAs and their 20 target genes were promising candidates for swine parturition and colostrum occurrence processes. Our research provided new insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.

• Korean Journal of Poultry Science
• /
• v.43 no.3
• /
• pp.149-157
• /
• 2016

This study was performed to investigate the effects of the stocking density (standard stocking density (SSD, $495cm^2/bird$)) vs. high stocking density (HSD,245cm2/bird) and challenge with lipopolysaccharide (LPS, 5mg/kg BW) on the stress-related physiological indicators in chicks. There was a significant (p<0.05) decrease in body weight, but not in the weight of immune organs, between the SSD and HSD groups. The LPS group resulted in a significant (p<0.05) increase in the weights of the thymus and bursa of fabricius compared with the SSD group. Plasma biochemical components, including aspartate transaminase (AST), alanine transaminase (ALT), blood urea nitrogen, Ca, P, creatine kinase and uric acid, markedly (p<0.05) increased in the LPS birds, although no difference in these parameters was observed between the SSD and HSD birds. Furthermore, the birds challenged with LPS showed a significant (p<0.05) increase in the plasma corticosterone level, although this hormone did not differ between the SSD and HSD groups. In the mRNA expression of pro-inflammatory cytokines, hepatic $IL-1{\beta}$, IL-6 and iNOS in the LPS group significantly (p<0.05) increased compared with those in the SSD group. Thymic mRNA expression of $IL-1{\beta}$, IL-6 and IL-18 in the LPS group also significantly (p<0.05) increased compared with those in the other groups. In addition, mRNA expression of $IL-1{\beta}$ in the bursa of fabricius of the LPS group increased (p<0.05) without affecting the other cytokines. Under high stocking density, thymic $IL-1{\beta}$ was the only cytokine that was up-regulated compared with the SSD group. In conclusion, an acute stress induced by LPS challenge profoundly affected immune organ weight, blood biochemical profiles and pro-inflammatory cytokine expression, while chronic stress did not markedly affect biochemical and immunological parameters, suggesting that chicks under high stocking density could be adapted to prolonged stressors.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.1
• /
• pp.154-161
• /
• 2007

Human immunodeficiency virus type 1 (HIV-1) infections are responsible for a substantial number of deaths annually and represent a significant threat to public health. According to the latest study, the Tat (Transactivator of transcription) protein is essential in transcription and replication of viral genes, and is among the early expression genes involved in the life cycle of HIV. The virion NC (nucleocapsid) plays an important role in early mRNA expression and contributes to the rapid viral replication that occurs during HIV-1 infection. Therefore, we attempted to elucidate the relationship between the Tat protein and nucleocapsid protein. In a comparison of two independently prepared and hybridized samples, flag NC overexpressed HEK 293T cells and pTat overexpressed HEK 293T cells, and hybridization showed the differences in expression in each case. Among the microarray results confirmed with real-time reverse transcriptase assay, twelve genes were identified to be involved according to their gene expression profiles. Of approximately 8,208 human genes that were analyzed, we monitored candidate genes that might have been related to NC and Tat genes from gene expression profiles. Additionally, the pathways could be viewed and analyzed through the use of Pathway Studio software. The pathways from the gene list were built and paths were found among the molecules/cell objects/processes by the curation method.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.74.1-74
• /
• 2003

Differential display (DD) of mRNA is a technique in which mRNA species expressed by a cell population are reverse transcribed and then amplified by many separate polymerase chain reactions (PCR). Using DD-RT-PCR we obtained many genes that expressed differentially in healthy and PVX-infected Nicotiana benthamima, using total RNAs extracted from healthy and PVX-infected N. benthamiana plants. Three hundred and twenty-five DNA fragments isolated from DD-RT-PCR were cloned and sequenced for further characterization. Several host genes including SKPI-like protein, heat shock transcription factor and Avr9/Cf-9 rapidly elicited protein were selected to obtain full-length open reading frame and to characterize their potential involvement in virus disease development and/or host's defense against virus infection employing PVX-based expression vector. Transcrips from wild-type and clones containing each selected gene were inoculated onto N. benthamiana Levels of virus replication were confirmedby RT-PCR and RNA blot analysis, Expression profiles and potential role(s) of selected genes upon PVX infection will be discussed.