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Transcriptional regulation

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https://www.readbyqxmd.com/read/28734156/a-novel-hypoxia-response-element-regulates-oxygen-related-repression-of-tissue-factor-pathway-inhibitor-in-the-breast-cancer-cell-line-mcf-7
#1
Xue Yan Cui, Grethe Skretting, Mari Tinholt, Benedicte Stavik, Anders Erik Astrup Dahm, Kristine Kleivi Sahlberg, Sandip Kanse, Nina Iversen, Per Morten Sandset
BACKGROUND: Hypoxia is one of the most pervasive physiological stresses in solid tumors. We have previously demonstrated that tissue factor (TF) pathway inhibitor (TFPI) expression was transcriptionally repressed by the activation of hypoxia inducible factor (HIF)-1α under hypoxic conditions. However, the role of HIF-2α, also known as endothelial PAS domain-containing protein 1 (EPAS1), on TFPI expression remains unclear. AIM: To explore the role of HIF-2α/EPAS1 in the regulation of TFPI expression under hypoxia in breast cancer cells...
July 14, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/28732385/the-role-of-mirna-and-lncrna-in-gastric-cancer
#2
REVIEW
Ning-Bo Hao, Ya-Fei He, Xiao-Qin Li, Kai Wang, Rui-Ling Wang
Gastric cancer is one of the most common cancers and has the highest mortality rate worldwide. It is worthwhile to explore the mechanism of gastric cancer progression. An increasing number of studies have found that non-coding RNAs including miRNA and lncRNA play important roles in gastric cancer progression. This review summarized the role of ectopic miRNA in gastric cancer proliferation, growth, migration, invasion and apoptosis. Meantime, aberrantly expressed miRNA also received a great deal of attention as potential biomarker for gastric cancer diagnosis and therapy...
July 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732356/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#3
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
July 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732347/histone-demethylase-jmjd2c-epigenetic-regulators-in-tumors
#4
REVIEW
Chengcheng Zhang, Zhongqi Wang, Qing Ji, Qi Li
Histone methylation is one of the major epigenetic modifications, and various histone methylases and demethylases participate in the epigenetic regulating. JMJD2C has been recently identified as one of the histone lysine demethylases. As one member of the Jumonji-C histone demethylase family, JMJD2C has the ability to demethylate tri- or di-methylated histone 3 and 2 in either K9 (lysine residue 9) or K36 (lysine residue 36) sites by an oxidative reaction, thereby affecting heterochromatin formation, genomic imprinting, X-chromosome inactivation, and transcriptional regulation of genes...
July 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732288/lncrna-hotair-alleviates-rheumatoid-arthritis-by-targeting-mir-138-and-inactivating-nf-%C3%AE%C2%BAb-pathway
#5
Hong-Ju Zhang, Qiao-Feng Wei, Shu-Jun Wang, Hong-Jie Zhang, Xiu-Ying Zhang, Qin Geng, Yan-Hui Cui, Xiu-Hua Wang
Rheumatoid arthritis (RA) is a chronic and autoimmune-mediated inflammatory disease. We aimed to investigate the regulation of lncRNA HOTAIR in LPS-treated chondrocytes and RA mouse. Our results showed that HOTAIR expression was significantly reduced in LPS-treated chondrocytes. The HOTAIR was then over-expressed in chondrocytes by transfecting recombinant lentivirus carrying sequences encoding HOTAIR. The LPS-induced reduction of cell proliferation rate and production of two inflammatory factors interleukin (IL)-17, IL-23 were markedly inhibited...
July 18, 2017: International Immunopharmacology
https://www.readbyqxmd.com/read/28732175/genome-wide-identification-functional-prediction-and-evolutionary-analysis-of-r2r3-myb-superfamily-in-brassica-napus
#6
Ali Hajiebrahimi, Hajar Owji, Shiva Hemmati
R2R3-MYBs are important transcription factors (TFs) in planta, involved in development and various stress conditions. Phylogenetic analysis showed the presence of 249 R2R3-MYB TFs in Brassica napus called BnaR2R3-MYBs, clustered into 38 clades. BnaR2R3-MYBs were distributed on 19 chromosomes of B. napus. Sixteen gene clusters were identified. BnaR2R3-MYBs were characterized by motif prediction, gene structure analysis and gene ontology. Evolutionary analysis revealed that BnaR2R3-MYBs are mainly formed as a result of whole genome duplication...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28732084/increased-parb-level-affects-expression-of-stress-response-adaptation-and-virulence-operons-and-potentiates-repression-of-promoters-adjacent-to-the-high-affinity-binding-sites-pars3-and-pars4-in-pseudomonas-aeruginosa
#7
Adam Kawalek, Krzysztof Glabski, Aneta Agnieszka Bartosik, Anna Fogtman, Grazyna Jagura-Burdzy
Similarly to its homologs in other bacteria, Pseudomonas aeruginosa partitioning protein ParB facilitates segregation of newly replicated chromosomes. Lack of ParB is not lethal but results in increased frequency of anucleate cells production, longer division time, cell elongation, altered colony morphology and defective swarming and swimming motility. Unlike in other bacteria, inactivation of parB leads to major changes of the transcriptome, suggesting that, directly or indirectly, ParB plays a role in regulation of gene expression in this organism...
2017: PloS One
https://www.readbyqxmd.com/read/28732076/eincr1-is-an-egf-inducible-lincrna-overexpressed-in-lung-adenocarcinomas
#8
Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, David T Gerrard, Neil A Hanley, Andrew D Sharrocks
Long non-coding RNAs are being increasingly recognised as important molecules involved in regulating a diverse array of biological functions. For example, many long non-coding RNAs have been associated with tumourigenesis and in this context their molecular functions often involves impacting on chromatin and transcriptional control processes. One important cellular control system that is often deregulated in cancer cells is the ERK MAP kinase pathway. Here we have investigated whether ERK pathway signaling in response to EGF stimulation, leads to changes in the production of long non-coding RNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28732013/the-kp1_4563-gene-is-regulated-by-the-camp-receptor-protein-and-controls-type-3-fimbrial-function-in-klebsiella-pneumoniae-ntuh-k2044
#9
Mei Luo, Shiya Yang, Xuan Li, Pin Liu, Jian Xue, Xipeng Zhou, Kewen Su, Xuan Xu, Ying Qing, Jingfu Qiu, Yingli Li
Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen that can adhere to host cells or extracellular matrix via type 1 and type 3 fimbriae. KP1_4563 is a gene encoding a hypothetical protein in K. pneumoniae NTUH-K2044. KP1_4563 is located between the type 1 and type 3 fimbrial gene clusters and is likely associated with fimbrial function given its putative conserved domains of unknown function (DUF1471). Cyclic AMP receptor protein (CRP) regulates virulence-related gene expression and is a crucial transcriptional regulator in many bacteria...
2017: PloS One
https://www.readbyqxmd.com/read/28731845/rho-protein-roles-and-mechanisms
#10
Pallabi Mitra, Gairika Ghosh, Md Hafeezunnisa, Ranjan Sen
At the end of the multistep transcription process, the elongating RNA polymerase (RNAP) is dislodged from the DNA template either at specific DNA sequences, called the terminators, or by a nascent RNA-dependent helicase, Rho. In Escherichia coli, about half of the transcription events are terminated by the Rho protein. Rho utilizes its RNA-dependent ATPase activities to translocate along the mRNA and eventually dislodges the RNAP via an unknown mechanism. The transcription elongation factor NusG facilitates this termination process by directly interacting with Rho...
July 21, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28731788/identification-of-osr2-transcriptional-target-genes-in-palate-development
#11
X Fu, J Xu, P Chaturvedi, H Liu, R Jiang, Y Lan
Previous studies have identified the odd-skipped related 2 (Osr2) transcription factor as a key intrinsic regulator of palatal shelf growth and morphogenesis. However, little is known about the molecular program acting downstream of Osr2 in the regulation of palatogenesis. In this study, we isolated palatal mesenchyme cells from embryonic day 12.5 (E12.5) and E13.5 Osr2(RFP/+) and Osr2(RFP/-) mutant mouse embryos and performed whole transcriptome RNA sequencing analyses. Differential expression analysis of the RNA sequencing datasets revealed that expression of 70 genes was upregulated and expression of 61 genes was downregulated by >1...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28731785/networks-of-transcription-factors-for-oct4-expression-in-mice
#12
Yu-Qiang Li
The present review aimed to assess the networks of transcription factors regulating the Oct4 expression in mice. Through a comprehensive analysis of the binding sites and the interrelationships of the transcription factors of Oct4, it is found that transcription factors of Oct4 form three regulating complexes centered by Oct4-Sox2, Nanog, and Lrh1. They bind on CR4, CR2, and CR1 regions of Oct4 promoter/enhancer, respectively, to activate Oct4 transcription synergistically. This article also discusses the mechanisms of fine-tuning the Oct4 expression...
July 21, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28731781/lncrna-pvt1-facilitates-invasion-through-upregulation-of-mmp9-in-nonsmall-cell-lung-cancer-cell
#13
Wei Chen, Huayun Zhu, Li Yin, Tingting Wang, Jianfeng Wu, Jianhua Xu, Hua Tao, Juying Liu, Xia He
Lung cancer is the most common solid tumor around the world. It has been reported that upregulation of long noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (lncRNA-PVT1) is closely associated with tumor metastasis. However, the function and underlying molecular mechanism of lncRNA-PVT1 in nonsmall cell lung cancer (NSCLC) invasion remain unknown. In this study, we found that overexpression of lncRNA-PVT1 promoted the invasive ability of NSCLC cells, whereas silence of lncRNA-PVT1 suppressed cell invasion...
July 21, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28731568/a-strong-hybrid-fatty-acid-inducible-transcriptional-sensor-built-from-yarrowia-lipolytica-upstream-activating-and-regulatory-sequences
#14
Murtaza Shabbir-Hussain, Ian Wheeldon, Mark A Blenner
The engineering of Yarrowia lipolytica to accumulate lipids with high titers and productivities has been enabled with a handful of constitutive promoters for pathway engineering. However, the development of promoters that are both strong and lipid responsive could greatly benefit the bioproduction efficiency of lipid-derived oleochemicals in oleaginous yeast. in this study, we sought to engineer a fatty acid regulated hybrid promoter for use in Y. lipolytica. We identified a 200 bp upstream regulatory sequence in the peroxisomal acyl CoA oxidase 2 (POX2) promoter...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731516/mir-181d-regulates-human-dendritic-cell-maturation-through-nf-%C3%AE%C2%BAb-pathway
#15
Xian Wei Su, Gang Lu, Chi Kwan Leung, Qiang Liu, Yi Li, Kam Sze Tsang, Shi Dou Zhao, Danny Tat Ming Chan, Hsiang Fu Kung, Wai Sang Poon
OBJECTIVES: MicroRNAs (miRNAs) are considered as the cellular regulators which post-transcriptionally modulate gene expression in diverse biological processes including cell development and immunity. In this study, we investigated functions of miR-181d in dendritic cells (DCs) maturation, and the underlying mechanisms were also explored. MATERIALS AND METHODS: Here we did the miRNA screening in human DCs in response to lipopolysaccharides (LPS) by quantitative real-time PCR (qRT-PCR)...
July 21, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28731468/a-role-for-the-cell-wall-protein-silacidin-in-cell-size-of-the-diatom-thalassiosira-pseudonana
#16
Amy R Kirkham, Patrick Richthammer, Katrin Schmidt, Martin Wustmann, Yoshiaki Maeda, René Hedrich, Eike Brunner, Tsuyoshi Tanaka, Karl-Heinz van Pée, Angela Falciatore, Thomas Mock
Diatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731347/integrated-venomics-and-venom-gland-transcriptome-analysis-of-juvenile-and-adult-mexican-rattlesnakes-crotalus-simus-c-tzabcan-and-c-culminatus-revealed-mirna-modulated-ontogenetic-shifts
#17
Jordi Durban, Libia Sanz, Dilza Trevisan-Silva, Edgar Neri-Castro, Alejandro Alagón, Juan Jose Calvete
Adult rattlesnakes within genus Crotalus express one of two distinct venom phenotypes, type I (haemorrhagic) and type II (neurotoxic). In Costa Rican Central American rattlesnake, ontogenetic changes in the concentration of miRNAs modulate venom type II to type I transition. Venomics and venom gland transcriptome analyses showed that adult C. simus and C. tzabcan expressed intermediate patterns between type II and type I venoms, whereas C. culminatus had a canonical type I venom. Neonate/juvenile and adult Mexican rattlesnakes showed notable inter- and intraspecific variability in the number, type, abundance and ontogenetic shifts of the transcriptional and translational venom gland activities...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28731287/tricetin-suppresses-human-oral-cancer-cell-migration-by-reducing-matrix-metalloproteinase-9-expression-through-the-mitogen-activated-protein-kinase-signaling-pathway
#18
Tsung-Te Chung, Chun-Yi Chuang, Ying-Hock Teng, Ming-Ju Hsieh, Ji-Ching Lai, Yi-Ting Chuang, Mu-Kuan Chen, Shun-Fa Yang
Tricetin is a flavonoid derivative and a potent anti-inflammatory and anticancer agent. However, the molecular mechanism underlying the effects of tricetin on human oral cancer cell migration remains unclear. The cell migration and invasion abilities of three oral cancer cell lines (SCC-9, HSC-3, and OECM-1) were analyzed using Boyden chamber migration assays. Our results demonstrated that tricetin attenuates 12-O-tetradecanoylphorbol-13-acetate-induced SCC-9, HSC-3, and OECM-1 cell invasiveness and migration by reducing matrix metalloproteinase (MMP)-9 enzyme activity...
July 21, 2017: Environmental Toxicology
https://www.readbyqxmd.com/read/28731260/transcriptional-regulation-of-app-by-apoe-to-boldly-go-where-no-isoform-has-gone-before-apoe-app-transcription-and-ad-hypothesised-mechanisms-and-existing-knowledge-gaps
#19
REVIEW
Liying Corinne Lee, Michele Q L Goh, Edward H Koo
Alzheimer's disease (AD) is the most common form of dementia that gradually disrupts the brain network to impair memory, language and cognition. While the amyloid hypothesis remains the leading proposed mechanism to explain AD pathophysiology, anti-amyloid therapeutic strategies have yet to translate into useful therapies, suggesting that amyloid β-protein and its precursor, the amyloid precursor protein (APP) are but a part of the disease cascade. Further, risk of AD can be modulated by a number of factors, the most impactful being the ɛ4 isoform of apolipoprotein E (apoE)...
July 21, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28731226/curcumin-converts-foxp3-regulatory-t-cells-to-t-helper-1-cells-in-patients-with-lung-cancer
#20
JianYong Zou, ChunHua Su, HongHe Luo, YiYan Lei, Bo Zeng, HaoShuai Zhu, ZhenGuang Chen
The regulatory T cells (Treg) play an important role in the tumor tolerance. The methods to regulate the Treg population in cancer-bearing hosts are limited currently. The effect of curcumin on inhibiting cancer has been recognized, but the mechanism remains elusive. This study tests a hypothesis that administration of curcumin down regulates Tregs in lung cancer (LC) patients. In this study, a group of LC patients was treated with curcumin. The peripheral Tregs and T helper (Th) 1 cells were analyzed by flow cytometry...
July 21, 2017: Journal of Cellular Biochemistry
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