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Gene expression regulation

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https://www.readbyqxmd.com/read/27933643/syntaxin-4a-regulates-matrix-vesicle-mediated-bone-matrix-production-by-osteoblasts
#1
Shinji Kawai, Ikumi Michikami, Jirouta Kitagaki, Kenji Hata, Hiroshi Kiyonari, Takaya Abe, Atsuo Amano, Satoshi Wakisaka
Osteoblasts secrete matrix vesicles and proteins to bone surfaces, though the molecular mechanisms of this secretion system remain unclear. The present findings reveal the roles of important genes in osteoblasts involved in regulation of extracellular matrix secretion. We especially focused on SNARE genes and identified notable Syntaxin 4a (Stx4a) expression on the basolateral side of the plasma membrane of osteoblasts. Furthermore, Stx4a overexpression was found to increase mineralization by osteoblastic cells, whereas Stx4a knockdown reduced levels of mineralization...
December 8, 2016: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/27933583/looking-beyond-the-5-httlpr-polymorphism-genetic-and-epigenetic-layers-of-regulation-affecting-the-serotonin-transporter-gene-expression
#2
REVIEW
Sandra Iurescia, Davide Seripa, Monica Rinaldi
Serotonin (5-HT) is a neurotransmitter that regulates fundamental aspects of brain development, physiology and behaviour. The serotonin transporter (5-HTT) is deputized to the reuptake of 5-HT from the intersynaptic space in the presynaptic neurons. 5-HTT governs duration and magnitude of 5-HT biological actions, acting as a master regulator of the fine-tuning of 5-HT signalling. Genetic variation at SLC6A4 gene locus, encoding 5-HTT, contributes to alteration in 5-HT reuptake. The 5-HTTLPR/rs25531/rs25532 polymorphisms located in the promoter region of SLC6A4 gene have been associated with stress-related psychopathology and functional brain phenotypes...
December 8, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27933539/systems-genetics-analysis-of-iron-and-its-regulation-in-brain-and-periphery
#3
Byron C Jones, Leslie C Jellen
In this contribution, we demonstrate the utility of the systems genetics-systems biology approach to the study of iron regulation while employing a comprehensive database. We describe our work in iron regulation in the brain and periphery under normal iron and iron-restricted dietary conditions in the BXD family of recombinant inbred mouse strains. Using multiple measures, we showed wide variation among the strains in the effect of being fed an iron-restricted diet for 100 days in every measure from brain and from the periphery...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933535/systems-genetics-analysis-to-identify-the-genetic-modulation-of-a-glaucoma-associated-gene
#4
Sumana R Chintalapudi, Monica M Jablonski
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933533/systems-genetics-as-a-tool-to-identify-master-genetic-regulators-in-complex-disease
#5
Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, Enrico Petretto
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933527/integrating-multidimensional-data-sources-to-identify-genes-regulating-complex-phenotypes
#6
Rupert W Overall
Phenotypes collected with a view to quantitative trait locus mapping can be augmented with compatible whole-transcriptome expression data and information from several other sources. These different data sources can be assembled into multidimensional network models which allow the identification of key genes potentially driving the phenotype of interest. The following chapter describes this approach using an example workflow. Several alternatives and potential limitations are discussed to aid the researcher when applying these techniques to their own work...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933526/epigenetics-and-control-of-rnas
#7
Henrike Maatz, Sebastiaan van Heesch, Franziska Kreuchwig, Allison Faber, Eleonora Adami, Norbert Hubner, Matthias Heinig
Histone modifications are epigenetic marks that fundamentally impact the regulation of gene expression. Integrating histone modification information in the analysis of gene expression traits (eQTL mapping) has been shown to significantly enhance the prediction of eQTLs. In this chapter, we describe (1) how to perform quantitative trait locus (QTL) analysis using histone modification levels as traits and (2) how to integrate these data with information on RNA expression for the elucidation of the epigenetic control of transcript levels...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933510/anti-fibrotic-effects-of-salvia-miltiorrhiza-and-ligustrazine-injection-on-lx-2-cells-involved-with-increased-n-myc-downstream-regulated-gene-2-expression
#8
Jin Zheng, Li-Tian Ma, Qin-You Ren, Yue Hu, Yang Bai, Huan Bian, Yi Zhang, Yong-Chun Zhou, Ming-Hui Yang
OBJECTIVE: To investigate the effects of Salvia miltiorrhiza and Ligustrazine Injection (SML) on proliferation and apoptosis of human hepatic stellate cell LX-2 and the expression of N-myc downstream-regulated gene 2 (NDRG2, a tumor suppressor gene). METHODS: HSCs from the LX-2 cell line were cultured in vitro. The proliferative state of different initial LX-2 cell numbers was measured using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay...
December 8, 2016: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/27933466/microrna-145-modulates-epithelial-mesenchymal-transition-and-suppresses-proliferation-migration-and-invasion-by-targeting-sip1-in-human-cervical-cancer-cells
#9
Anusha Sathyanarayanan, Karthik Subramanian Chandrasekaran, Devarajan Karunagaran
PURPOSE: Previously, it has been reported that microRNA-145 (miR-145) is lowly expressed in human cervical cancers and that its putative tumour suppressive role may be attributed to epithelial-mesenchymal transition (EMT) regulation. Here, we aimed to assess whether miR-145 may affect EMT-associated markers/genes and suppress cervical cancer growth and motility, and to provide a mechanistic basis for these phenomena. METHODS: The identification of the SMAD-interacting protein 1 (SIP1) mRNA as putative miR-145 target was investigated using a 3' untranslated region (3'UTR) luciferase assay and Western blotting, respectively...
December 8, 2016: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/27933404/genome-wide-high-content-sirna-screening-identifies-the-alzheimer-s-genetic-risk-factor-fermt2-as-a-major-modulator-of-app-metabolism
#10
Julien Chapuis, Amandine Flaig, Benjamin Grenier-Boley, Fanny Eysert, Virginie Pottiez, Gaspard Deloison, Alexandre Vandeputte, Anne-Marie Ayral, Tiago Mendes, Shruti Desai, Alison M Goate, John S K Kauwe, Florence Leroux, Adrien Herledan, Florie Demiautte, Charlotte Bauer, Fréderic Checler, Ronald C Petersen, Kaj Blennow, Henrik Zetterberg, Lennart Minthon, Vivianna M Van Deerlin, Virginia Man-Yee Lee, Leslie M Shaw, John Q Trojanowski, Marilyn Albert, Abhay Moghekar, Richard O'Brien, Elaine R Peskind, Nicolas Malmanche, Gerard D Schellenberg, Pierre Dourlen, Ok-Ryul Song, Carlos Cruchaga, Philippe Amouyel, Benoit Deprez, Priscille Brodin, Jean-Charles Lambert
Genome-wide association studies (GWASs) have identified 19 susceptibility loci for Alzheimer's disease (AD). However, understanding how these genes are involved in the pathophysiology of AD is one of the main challenges of the "post-GWAS" era. At least 123 genes are located within the 19 susceptibility loci; hence, a conventional approach (studying the genes one by one) would not be time- and cost-effective. We therefore developed a genome-wide, high-content siRNA screening approach and used it to assess the functional impact of gene under-expression on APP metabolism...
December 8, 2016: Acta Neuropathologica
https://www.readbyqxmd.com/read/27933318/global-analysis-and-comparison-of-the-transcriptomes-and-proteomes-of-group-a-streptococcus-biofilms
#11
Jeffrey A Freiberg, Yoann Le Breton, Bao Q Tran, Alison J Scott, Janette M Harro, Robert K Ernst, Young Ah Goo, Emmanuel F Mongodin, David R Goodlett, Kevin S McIver, Mark E Shirtliff
To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points...
November 2016: MSystems
https://www.readbyqxmd.com/read/27933310/dynamics-of-antigen-presentation-to-transgene-product-specific-cd4-t-cells-and-of-treg-induction-upon-hepatic-aav-gene-transfer
#12
George Q Perrin, Irene Zolotukhin, Alexandra Sherman, Moanaro Biswas, Ype P de Jong, Cox Terhorst, Andrew M Davidoff, Roland W Herzog
The tolerogenic hepatic microenvironment impedes clearance of viral infections but is an advantage in viral vector gene transfer, which often results in immune tolerance induction to transgene products. Although the underlying tolerance mechanism has been extensively studied, our understanding of antigen presentation to transgene product-specific CD4(+) T cells remains limited. To address this, we administered hepatotropic adeno-associated virus (AAV8) vector expressing cytoplasmic ovalbumin (OVA) into wt mice followed by adoptive transfer of transgenic OVA-specific T cells...
2016: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/27933223/epigenetic-editing-on-the-verge-of-reprogramming-gene-expression-at-will
#13
REVIEW
David Cano-Rodriguez, Marianne G Rots
Genome targeting has quickly developed as one of the most promising fields in science. By using programmable DNA-binding platforms and nucleases, scientists are now able to accurately edit the genome. These DNA-binding tools have recently also been applied to engineer the epigenome for gene expression modulation. Such epigenetic editing constructs have firmly demonstrated the causal role of epigenetics in instructing gene expression. Another focus of epigenome engineering is to understand the order of events of chromatin remodeling in gene expression regulation...
2016: Current Genetic Medicine Reports
https://www.readbyqxmd.com/read/27933082/rna-seq-transcriptome-response-of-flax-linum-usitatissimum-l-to-the-pathogenic-fungus-fusarium-oxysporum-f-sp-lini
#14
Leonardo Galindo-González, Michael K Deyholos
Fusarium oxysporum f. sp. lini is a hemibiotrophic fungus that causes wilt in flax. Along with rust, fusarium wilt has become an important factor in flax production worldwide. Resistant flax cultivars have been used to manage the disease, but the resistance varies, depending on the interactions between specific cultivars and isolates of the pathogen. This interaction has a strong molecular basis, but no genomic information is available on how the plant responds to attempted infection, to inform breeding programs on potential candidate genes to evaluate or improve resistance across cultivars...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933081/the-density-and-length-of-root-hairs-are-enhanced-in-response-to-cadmium-and-arsenic-by-modulating-gene-expressions-involved-in-fate-determination-and-morphogenesis-of-root-hairs-in-arabidopsis
#15
Ramin Bahmani, Dong G Kim, Jin A Kim, Seongbin Hwang
Root hairs are tubular outgrowths that originate from epidermal cells. Exposure of Arabidopsis to cadmium (Cd) and arsenic [arsenite, As(III)] increases root hair density and length. To examine the underlying mechanism, we measured the expression of genes involved in fate determination and morphogenesis of root hairs. Cd and As(III) downregulated TTG1 and GL2 (negative regulators of fate determination) and upregulated GEM (positive regulator), suggesting that root hair fate determination is stimulated by Cd and As(III)...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933076/overexpression-of-tanac2d-displays-opposite-responses-to-abiotic-stresses-between-seedling-and-mature-stage-of-transgenic-arabidopsis
#16
Quanjun Huang, Yan Wang
Environmental stresses frequently affect plant growth and development, and many genes have been found to be induced by unfavorable environmental conditions. Here, we reported the biological functions of TaNAC2D, a stress-related NAC (NAM, ATAF, and CUC) gene from wheat. TaNAC2D showed transcriptional activator activity in yeast. TaNAC2D-GFP fusion protein was localized in the nucleus of wheat mesophyll protoplasts. TaNAC2D transcript abundance was significantly induced by NaCl, PEG6000, and abscisic acid (ABA) at seedling stage, and repressed by NaCl and PEG6000 at mature plant stage...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933071/stress-mediated-cis-element-transcription-factor-interactions-interconnecting-primary-and-specialized-metabolism-in-planta
#17
REVIEW
S A Sheshadri, M J Nishanth, Bindu Simon
Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933070/transcriptional-responses-in-root-and-leaf-of-prunus-persica-under-drought-stress-using-rna-sequencing
#18
Najla Ksouri, Sergio Jiménez, Christina E Wells, Bruno Contreras-Moreira, Yolanda Gogorcena
Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933067/peptide-idr-1002-inhibits-nf-%C3%AE%C2%BAb-nuclear-translocation-by-inhibition-of-i%C3%AE%C2%BAb%C3%AE-degradation-and-activates-p38-erk1-2-msk1-dependent-creb-phosphorylation-in-macrophages-stimulated-with-lipopolysaccharide
#19
Alejandro Huante-Mendoza, Octavio Silva-García, Javier Oviedo-Boyso, Robert E W Hancock, Víctor M Baizabal-Aguirre
The inflammatory response is a critical molecular defense mechanism of the innate immune system that mediates the elimination of disease-causing bacteria. Repair of the damaged tissue, and the reestablishment of homeostasis, must be accomplished after elimination of the pathogen. The innate defense regulators (IDRs) are short cationic peptides that mimic natural host defense peptides and are effective in eliminating pathogens by enhancing the activity of the immune system while controlling the inflammatory response...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27933063/aire-downregulation-is-associated-with-changes-in-the-posttranscriptional-control-of-peripheral-tissue-antigens-in-medullary-thymic-epithelial-cells
#20
Ernna H Oliveira, Claudia Macedo, Cristhianna V Collares, Ana Carolina Freitas, Paula Barbim Donate, Elza T Sakamoto-Hojo, Eduardo A Donadi, Geraldo A Passos
Autoimmune regulator (Aire) is a transcriptional regulator of peripheral tissue antigens (PTAs) and microRNAs (miRNAs) in medullary thymic epithelial cells (mTECs). In this study, we tested the hypothesis that Aire also played a role as an upstream posttranscriptional controller in these cells and that variation in its expression might be associated with changes in the interactions between miRNAs and the mRNAs encoding PTAs. We demonstrated that downregulation of Aire in vivo in the thymuses of BALB/c mice imbalanced the large-scale expression of these two RNA species and consequently their interactions...
2016: Frontiers in Immunology
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