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Modeling gene regulation

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https://www.readbyqxmd.com/read/29236331/reduction-of-histone-marks-h3k9me3-and-h3k27me3-by-epidrug-induces-neuroendocrine-differentiation-in-prostate-cancer
#1
Eunsohl Lee, Jingcheng Wang, Younghun Jung, Frank C Cackowski, Russell S Taichman
Neuroendocrine prostate cancer (NE PCa) is an aggressive malignancy, often presenting with advanced metastasis. We previously reported that reduction of histone marks regulated by DNMT1 following epidrug (5-Azacitidine, 5-Aza) treatment controls induction of epithelial to mesenchymal (EMT) and a cancer stem cell (CSC) phenotype, which facilitates tumorigenesis in PCa cells. Here, we use the epidrug 5-Aza as a model for how histone marks may regulate the reprogramming of prostate adenocarcinoma into NE phenotypic cells...
December 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29236320/analgesic-effects-of-microrna-129-5p-against-bone-cancer-pain-through-the-ephb1-ephrinb2-signaling-pathway-in-mice
#2
Shao-Nan Yu, Gui-Feng Liu, Long-Yun Li, Guo-Qing Zhao, Lin Liu, Xue-Feng Li
The study aims to investigate the analgesic effects of microRNA-129-5p (miR-129-5p) on bone cancer pain (BCP) by targeting Eph receptor B1 (EphB1) through the EphB1/EphrinB2 signaling pathway. BCP mice models were established, and C3H/HeJ female mice were classified into the normal, blank, negative control (NC), miR-129-5p mimics, miR-129-5p inhibitors, EphB1 knockout (KO), and miR-129-5p inhibitors + EphB1 KO groups. RT-qPCR and western blotting were used to evaluate miR-129-5p expression, and mRNA and protein expressions of EphB1, p-EphB1, EphrinB2 and p-EphrinB2...
December 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29236160/ethanol-and-cytokines-in-the-central-nervous-system
#3
Marisa Roberto, Reesha R Patel, Michal Bajo
The innate immune system plays a critical role in the ethanol-induced neuroimmune response in the brain. Ethanol initiates the innate immune response via activation of the innate immune receptors Toll-like receptors (TLRs, e.g., TLR4, TLR3, TLR7) and NOD-like receptors (inflammasome NLRs) leading to a release of a plethora of chemokines and cytokines and development of the innate immune response. Cytokines and chemokines can have pro- or anti-inflammatory properties through which they regulate the immune response...
December 14, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/29236054/genome-wide-profiling-of-small-rnas-and-degradome-revealed-conserved-regulations-of-mirnas-on-auxin-responsive-genes-during-fruit-enlargement-in-peaches
#4
Mengya Shi, Xiao Hu, Yu Wei, Xu Hou, Xue Yuan, Jun Liu, Yueping Liu
Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA)...
December 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29235574/ten-principles-of-heterochromatin-formation-and-function
#5
REVIEW
Robin C Allshire, Hiten D Madhani
Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression...
December 13, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29235503/inactivation-of-the-dnak-gene-in-clostridium-difficile-630-%C3%AE-erm-yields-a-temperature-sensitive-phenotype-and-increases-biofilm-forming-ability
#6
Shailesh Jain, Deborah Smyth, Barry M G O'Hagan, John T Heap, Geoff McMullan, Nigel P Minton, Nigel G Ternan
Clostridium difficile infection is a growing problem in healthcare settings worldwide and results in a considerable socioeconomic impact. New hypervirulent strains and acquisition of antibiotic resistance exacerbates pathogenesis; however, the survival strategy of C. difficile in the challenging gut environment still remains incompletely understood. We previously reported that clinically relevant heat-stress (37-41 °C) resulted in a classical heat-stress response with up-regulation of cellular chaperones...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235493/small-molecules-related-to-adrenomedullin-reduce-tumor-burden-in-a-mouse-model-of-colitis-associated-colon-cancer
#7
Laura Ochoa-Callejero, Josune García-Sanmartín, Sonia Martínez-Herrero, Susana Rubio-Mediavilla, Judit Narro-Íñiguez, Alfredo Martínez
To investigate the contribution of adrenomedullin (AM) and its gene-related peptide, proadrenomedullin N-terminal 20 peptide (PAMP), to the progression and potential treatment of colon cancer we studied the effects of four small molecules (SM) related to AM and PAMP on a mouse model of colon cancer. For each SM, four experimental groups of male mice were used: (i) Control group; (ii) SM group; (iii) DSS group (injected with azoxymethane [AOM] and drank dextran sulfate sodium [DSS]); and (iv) DSS + SM group (treated with AOM, DSS, and the SM)...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235426/cpda-is-involved-in-amino-acid-metabolism-in-shewanella-oneidensis-mr-1
#8
Takuya Kasai, Atsushi Kouzuma, Kazuya Watanabe
Cyclic 3',5'-adenosine monophosphate (cAMP) phosphodiesterase (CPD) is an enzyme that catalyzes the hydrolysis of cAMP, a signaling molecule affecting diverse cellular and metabolic processes in bacteria. Some CPDs are also known to function in cAMP-independent manners, while their physiological roles remain largely unknown. Here, we investigated physiological roles of CPD in Shewanella oneidensis MR-1, a model environmental bacterium, and report that CPD is involved in amino-acid metabolism. We found that a CPD-deficient mutant of MR-1 (ΔcpdA) showed decreased expression of genes for the synthesis of methionine, S-adenosylmethionine, and histidine and required these three compounds to grow in minimal media...
December 13, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29235416/skeletal-muscle-cell-contraction-reduces-a-novel-myokine-chemokine-c-x-c-motif-ligand-10-cxcl10-potential-roles-in-exercise-regulated-angiogenesis
#9
Yuri Ishiuchi, Hitoshi Sato, Kazuki Tsujimura, Hideo Kawaguchi, Takashi Matsuwaki, Keitaro Yamanouchi, Masugi Nishihara, Taku Nedachi
Accumulating evidence indicates that skeletal muscle secrets proteins referred to as myokines and that exercise contributes to their regulation. In this study, we propose that chemokine (C-X-C motif) ligand 10 (CXCL10) functions as a novel myokine. Initially, we stimulated differentiated C2C12 myotubes with or without electrical pulse stimulation (EPS) to identify novel myokines. Cytokine array analysis revealed that CXCL10 secretion was significantly reduced by EPS, which was further confirmed by enzyme-linked immunosorbent assay and quantitative polymerase chain reaction analysis...
December 13, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29235098/hepcidin-and-dna-promoter-methylation-in-hepatocellular-carcinoma
#10
Silvia Udali, Annalisa Castagna, Michela Corbella, Andrea Ruzzenente, Sara Moruzzi, Filippo Mazzi, Tommaso Campagnaro, Domenica De Santis, Antonia Franceschi, Patrizia Pattini, Rossella Gottardo, Oliviero Olivieri, Luigi Perbellini, Alfredo Guglielmi, Sang-Woon Choi, Domenico Girelli, Simonetta Friso
BACKGROUND: The liver hormone hepcidin regulates iron homeostasis that is often altered in hepatocellular carcinoma (HCC). Epigenetic phenomena control gene expression through a dynamic fashion, therefore, considering the plasticity of both iron homeostasis and epigenetic mechanisms and their role in liver carcinogenesis, we investigated whether hepcidin gene (HAMP) expression is modulated by DNA methylation thus affecting iron status in human HCC. MATERIALS AND METHODS: Thirty-two patients affected by non-viral HCC were enrolled and their main clinical and biochemical characteristics obtained...
December 13, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29234458/robust-genetic-transformation-of-sorghum-sorghum-bicolor-l-using-differentiating-embryogenic-callus-induced-from-immature-embryos
#11
Srinivas Belide, Thomas Vanhercke, James Robertson Petrie, Surinder Pal Singh
Background: Sorghum (Sorghum bicolor L.) is one of the world's most important cereal crops grown for multiple applications and has been identified as a potential biofuel crop. Despite several decades of study, sorghum has been widely considered as a recalcitrant major crop for transformation due to accumulation of phenolic compounds, lack of model genotypes, low regeneration frequency and loss of regeneration potential through sub-cultures. Among different explants used for genetic transformation of sorghum, immature embryos are ideal over other explants...
2017: Plant Methods
https://www.readbyqxmd.com/read/29234407/jinhong-tablet-reduces-damage-of-intestinal-mucosal-barrier-in-rats-with-acute-biliary-infection-via-bcl-2-bax-mrna-and-protein-regulation
#12
Xiaoqiang Liang, Xiao Ni, YongQi Wang, Jinkun Xie, Xuelin Zhang, Honggang Gu, Jingzhe Zhang
Objective: To explore the effects and mechanism of Jinhong Tablet on intestinal mucosal barrier function and SIRS in rats with acute biliary infection. Methods: 36 SD male rats were divided into three groups: sham operation (control), acute biliary infection (ABI) model, and Jinhong Tablet (Jinhong) group. Jinhong group were force-fed with Jinhong Tablet, while the other two groups received oral saline. At days 3 and 5, morphological changes of intestinal mucosa were assessed...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/29234348/diurnal-transcriptome-and-gene-network-represented-through-sparse-modeling-in-brachypodium-distachyon
#13
Satoru Koda, Yoshihiko Onda, Hidetoshi Matsui, Kotaro Takahagi, Yukiko Yamaguchi-Uehara, Minami Shimizu, Komaki Inoue, Takuhiro Yoshida, Tetsuya Sakurai, Hiroshi Honda, Shinto Eguchi, Ryuei Nishii, Keiichi Mochida
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29234285/a-microarray-study-of-carpet-shell-clam-ruditapes-decussatus-shows-common-and-organ-specific-growth-related-gene-expression-differences-in-gills-and-digestive-gland
#14
Carlos Saavedra, Massimo Milan, Ricardo B Leite, David Cordero, Tomaso Patarnello, M Leonor Cancela, Luca Bargelloni
Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29234048/gene-length-as-a-regulator-for-ribosome-recruitment-and-protein-synthesis-theoretical-insights
#15
Lucas D Fernandes, Alessandro P S de Moura, Luca Ciandrini
Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we propose transcript length as a further key determinant of translation efficiency. Based on a physical model that considers the kinetics of ribosomes advancing on the mRNA and diffusing in its surrounding, as well as mRNA circularisation and ribosome drop-off, we explain how the transcript length may play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233972/irf8-dependent-molecular-complexes-control-the-th9-transcriptional-program
#16
Etienne Humblin, Marion Thibaudin, Fanny Chalmin, Valentin Derangère, Emeric Limagne, Corentin Richard, Richard A Flavell, Sandy Chevrier, Sylvain Ladoire, Hélène Berger, Romain Boidot, Lionel Apetoh, Frédérique Végran, François Ghiringhelli
Interferon regulatory factors (IRF) have critical functions in lymphoid development and in immune response regulation. Although many studies have described the function of IRF4 in CD4+ T cells, few have focused on the IRF4 homologue, IRF8. Here, we show that IRF8 is required for Th9 differentiation in vitro and in vivo. IRF8 functions through a transcription factor complex consisting of IRF8, IRF4, PU.1 and BATF, which binds to DNA and boosts Il9 transcription. By contrast, IRF8 deficiency promotes the expression of other genes such as Il4, as IRF8 dimerises with the transcriptional repressor ETV6 and inhibits Il4 expression...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233860/pathway-analysis-of-transcriptomic-data-shows-immunometabolic-effects-of-vitamin-d
#17
Amadeo Muñoz Garcia, Martina Kutmon, Lars Eijssen, Martin Hewison, Chris T Evelo, Susan L Coort
Unbiased genomic screening analyses have highlighted novel immunomodulatory properties of the active form of vitamin D, 1,25-dihydroxyvitamin D (1,25(OH)2D). However, clearer interpretation of the resulting gene expression data is limited by cell model specificity. The aim of the current study was to provide a broader perspective on common gene regulatory pathways associated with innate immune responses to 1,25(OH)2D, through systematic re-interrogation of existing gene expression databases from multiple related monocyte models (the THP-1 monocytic cell line (THP-1), monocyte-derived dendritic cells (DCs), and monocytes)...
December 12, 2017: Journal of Molecular Endocrinology
https://www.readbyqxmd.com/read/29233754/molecular-characterization-tissue-distribution-and-differential-nutritional-regulation-of-putative-elovl5-elongase-in-silver-barb-puntius-gonionotus
#18
Madhusmita Nayak, Avinash Pradhan, Shiba Shankar Giri, Mrinal Samanta, V Badireenath Konkimalla, Ashis Saha
Fatty acid desaturase (Fads) and elongase (Elovl) are two important enzymes involved in the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs) in fishes. Silver barb (Puntius gonionotus) is considered a promising medium carp species for freshwater aquaculture in Asia. Earlier, Δ6 fads cDNA was characterized to understand the molecular mechanism of LC-PUFA biosynthesis in this species. In the present study elovl5-like elongase full-length cDNA was cloned and characterized by RACE (rapid amplification of cDNA ends), and analyzed its basal expression in various organs/tissues by quantitative real time PCR (qRT-PCR) assay...
December 9, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29233090/dna-methylation-regulates-discrimination-of-enhancers-from-promoters-through-a-h3k4me1-h3k4me3-seesaw-mechanism
#19
Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J Taft, Hans R Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J Araúzo-Bravo
BACKGROUND: DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. RESULTS: We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci...
December 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29233047/rnai-of-grp78-may-disturb-the-fusion-of-icr-mouse-palate-cultured-in-vitro
#20
C Ren, X Li, X Li, Y Xie, H Fu, Z Yan, Y Zhu
RNA interference (RNAi) is a powerful tool to silence or minimize gene expression, and palate culture in vitro is an important technique for study of the palate development. Our previous study demonstrated that the gene expression of glucose-regulated protein-78 (Grp78) was downregulation in the all-trans retinoic acid-induced mouse models of cleft palate (CP) during embryogenesis. To find the role of Grp78, the small interfering RNA (siRNA) of this gene carried by fluorescent vector was injected with a microinjector, through which about 30 pmol siRNA was injected into the Institute of Cancer Research (ICR) mouse palate explants...
January 1, 2017: Human & Experimental Toxicology
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