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eukaryotic gene regulation

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https://www.readbyqxmd.com/read/28340042/effects-of-dietary-l-arginine-levels-on-small-intestine-protein-turnover-and-the-expression-of-genes-related-to-protein-synthesis-and-proteolysis-of-layers
#1
L P Miao, C Yuan, X Y Dong, X Y Zhang, M Y Zhou, X T Zou
The aim of this study was to test the effects of dietary L-arginine (Arg) levels on protein turnover in the small intestine and the expression of genes related to protein synthesis and proteolysis of laying hens. Xinyang Black commercial laying hens (n = 864, aged 217 d) were randomly distributed to 6 treatments with 4 replicates of 36 birds. The dietary treatments were corn-corn gluten meal based diets containing 0.64, 0.86, 1.03, 1.27, 1.42 and 1.66% L-Arg, respectively. Fractional protein synthesis rate (FSR) and fractional protein gain rate (FGR) in the jejunum were the highest in the 1...
March 9, 2017: Poultry Science
https://www.readbyqxmd.com/read/28334975/apricot-an-integrated-computational-pipeline-for-the-sequence-based-identification-and-characterization-of-rna-binding-proteins
#2
Malvika Sharan, Konrad U Förstner, Ana Eulalio, Jörg Vogel
RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334892/inhibition-of-homologous-phosphorolytic-ribonucleases-by-citrate-may-represent-an-evolutionarily-conserved-communicative-link-between-rna-degradation-and-central-metabolism
#3
Carlanne M Stone, Louise E Butt, Joshua C Bufton, Daniel C Lourenco, Darren M Gowers, Andrew R Pickford, Paul A Cox, Helen A Vincent, Anastasia J Callaghan
Ribonucleases play essential roles in all aspects of RNA metabolism, including the coordination of post-transcriptional gene regulation that allows organisms to respond to internal changes and environmental stimuli. However, as inherently destructive enzymes, their activity must be carefully controlled. Recent research exemplifies the repertoire of regulatory strategies employed by ribonucleases. The activity of the phosphorolytic exoribonuclease, polynucleotide phosphorylase (PNPase), has previously been shown to be modulated by the Krebs cycle metabolite citrate in Escherichia coli...
March 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334833/chip-seq-analysis-of-the-luxr-type-regulator-vjbr-reveals-novel-insights-into-the-brucella-virulence-gene-expression-network
#4
Claudia L Kleinman, Gabriela Sycz, Hernán R Bonomi, Romina M Rodríguez, Angeles Zorreguieta, Rodrigo Sieira
LuxR-type transcription factors control diverse physiological functions necessary for bacterial adaptation to environmental changes. In the intracellular pathogen Brucella, the LuxR homolog VjbR has been shown to regulate the expression of virulence factors acting at early stages of the intracellular infection and, directly or indirectly, hundreds of additional genes. However, the precise determination of VjbR direct targets has so far proved elusive. Here, we performed chromatin immunoprecipitation of VjbR followed by next-generation sequencing (ChIP-seq)...
March 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334785/amino-acid-substitution-equivalent-to-human-chorea-acanthocytosis-i2771r-in-yeast-vps13-protein-affects-its-binding-to-phosphatidylinositol-3-phosphate
#5
Weronika Rzepnikowska, Krzysztof Flis, Joanna Kaminska, Marcin Grynberg, Agnieszka Urbanek, Kathryn R Ayscough, Teresa Zoladek
The rare human disorder chorea-acanthocytosis (ChAc) is caused by mutations in hVPS13A gene. The hVps13A protein interacts with actin and regulates the level of phosphatidylinositol 4-phosphate (PI4P) in the membranes of neuronal cells. Yeast Vps13 is involved in vacuolar protein transport and, like hVps13A, participates in PI4P metabolism. Vps13 proteins are conserved in eukaryotes, but their molecular function remains unknown. One of the mutations found in ChAc patients causes amino acids substitution I2771R which affects the localization of hVps13A in skeletal muscles...
March 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334074/genome-wide-analysis-reveals-that-exon-methylation-facilitates-its-selective-usage-in-the-human-transcriptome
#6
Shengli Li, Jiwei Zhang, Shenglin Huang, Xianghuo He
DNA methylation, especially in promoter regions, is a well-characterized epigenetic marker related to gene expression regulation in eukaryotes. However, the role of intragenic DNA methylation in the usage of corresponding exons still remains elusive. In this study, we described the DNA methylome across 10 human tissues. The human genome showed both conserved and varied methylation levels among these tissues. We found that the methylation densities in promoters and first exons were negatively correlated with the corresponding gene expression level...
February 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333290/evolution-of-the-genome-3d-organization-comparison-of-fused-and-segregated-globin-gene-clusters
#7
Anastasia P Kovina, Natalia V Petrova, Ekaterina S Gushchanskaya, Konstantin V Dolgushin, Evgeny S Gerasimov, Aleksandra A Galitsyna, Alexey A Penin, Ilya M Flyamer, Elena S Ioudinkova, Alexey A Gavrilov, Yegor S Vassetzky, Sergey V Ulianov, Olga V Iarovaia, Sergey V Razin
The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here we have studied the 3D organization and regulation of zebrafish globin domain and compared its organization and regulation with those of other vertebrate species. In birds and mammals, the alpha- and beta-globin genes are segregated into separate clusters located on different chromosomes and organized into chromatin domains of different types, whereas in cold-blooded vertebrates, including Danio rerio, alpha- and beta-globin genes are organized into common clusters...
March 7, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28331096/comprehensive-transcriptome-analyses-reveal-that-potato-spindle-tuber-viroid-triggers-genome-wide-changes-in-alternative-splicing-inducible-trans-acting-activity-of-phasirnas-and-immune-responses
#8
Yi Zheng, Ying Wang, Biao Ding, Zhangjun Fei
Many pathogens express non-coding RNAs (ncRNAs) during infection processes. In the most extreme case, pathogenic ncRNAs alone (such as viroids) can infect eukaryotic organisms leading to diseases. While a few of pathogenic ncRNAs have been implicated in regulating gene expression, functions of most pathogenic ncRNAs in host-pathogen interactions remain unclear. Here we employ potato spindle tuber viroid (PSTVd)-infecting tomato as a system to dissect host interactions with pathogenic ncRNAs, using comprehensive transcriptome analyses...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28329689/the-human-cchc-type-zinc-finger-nucleic-acid-binding-protein-binds-g-rich-elements-in-target-mrna-coding-sequences-and-promotes-translation
#9
Daniel Benhalevy, Sanjay K Gupta, Charles H Danan, Suman Ghosal, Hong-Wei Sun, Hinke G Kazemier, Katrin Paeschke, Markus Hafner, Stefan A Juranek
The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28327787/overexpression-of-mir-484-and-mir-744-in-vero-cells-alters-dengue-virus-replication
#10
Juan Camilo Castrillón-Betancur, Silvio Urcuqui-Inchima
BACKGROUND: Dengue is considered one of the world's most important mosquito-borne diseases. MicroRNAs (miRNAs) are small non-coding single-stranded RNAs that play an important role in the regulation of gene expression in eukaryotes. Although miRNAs possess antiviral activity against many mammalian-infecting viruses, their involvement in Dengue virus (DENV) replication remains poorly understood. OBJECTIVE: To determine the role of miR-484 and miR-744 in DENV infection and to examine whether DENV infection alters the expression of both miRNAs...
April 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28326294/the-eukaryote-like-serine-threonine-kinase-stk-regulates-the-growth-and-metabolism-of-zoonotic-streptococcus-suis
#11
Chunyan Zhang, Wen Sun, Meifang Tan, Mengmeng Dong, Wanquan Liu, Ting Gao, Lu Li, Zhuofei Xu, Rui Zhou
Like eukaryotes, bacteria express one or more serine/threonine kinases (STKs) that initiate diverse signaling networks. The STK from Streptococcus suis is encoded by a single-copy stk gene, which is crucial in stress response and virulence. To further understand the regulatory mechanism of STK in S. suis, a stk deletion strain (Δstk) and its complementary strain (CΔstk) were constructed to systematically decode STK characteristics by applying whole transcriptome RNA sequencing (RNA-Seq) and phosphoproteomic analysis...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28326098/nuclear-actin-in-development-and-transcriptional-reprogramming
#12
REVIEW
Shinji Misu, Marina Takebayashi, Kei Miyamoto
Actin is a highly abundant protein in eukaryotic cells and dynamically changes its polymerized states with the help of actin-binding proteins. Its critical function as a constituent of cytoskeleton has been well-documented. Growing evidence demonstrates that actin is also present in nuclei, referred to as nuclear actin, and is involved in a number of nuclear processes, including transcriptional regulation and chromatin remodeling. The contribution of nuclear actin to transcriptional regulation can be explained by its direct interaction with transcription machineries and chromatin remodeling factors and by controlling the activities of transcription factors...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28325876/comprehensive-and-quantitative-mapping-of-rna-protein-interactions-across-a-transcribed-eukaryotic-genome
#13
Richard She, Anupam K Chakravarty, Curtis J Layton, Lauren M Chircus, Johan O L Andreasson, Nandita Damaraju, Peter L McMahon, Jason D Buenrostro, Daniel F Jarosz, William J Greenleaf
RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptome-wide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the Saccharomyces cerevisiae genome...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28323924/guanabenz-sensitizes-pancreatic-%C3%AE-cells-to-lipotoxic-endoplasmic-reticulum-stress-and-apoptosis
#14
Baroj Abdulkarim, Miriam Hernangomez, Mariana Igoillo Esteve, Daniel A Cunha, Lorella Marselli, Piero Marchetti, Laurence Ladriere, Miriam Cnop
Deficient as well as excessive/prolonged endoplasmic reticulum (ER) stress signaling can lead to pancreatic β cell failure and the development of diabetes. Saturated free fatty acids (FFAs) such as palmitate induce lipotoxic ER stress in pancreatic β cells. One of the main ER stress response pathways is under the control of the protein kinase R-like endoplasmic reticulum kinase (PERK), leading to phosphorylation of the eukaryotic translation initiation factor 2 (eIF2α). The antihypertensive drug guanabenz has been shown to inhibit eIF2α dephosphorylation and protect cells from ER stress...
March 1, 2017: Endocrinology
https://www.readbyqxmd.com/read/28322466/the-role-of-mir-497-eif3a-axis-in-tgf%C3%AE-1-induced-epithelial-mesenchymal-transition-and-extracellular-matrix-in-rat-alveolar-epithelial-cells-and-pulmonary-fibroblasts
#15
Ren Guo, Yu Lv, Yang Ouyang, Siyu Liu, Dai Li
Multi-cause-induced interstitial lung disease, particularly pulmonary fibrosis, is a serious clinical concern. fibroblasts have been suggested to have a major role, with it recently being revealed that some of these fibroblasts are derived from alveolar epithelial cells through epithelial-mesenchymal transition (EMT). Eukaryotic translation initiation factor 3 subunit A (EIF3A) is a protein that in humans is encoded by the EIF3A gene, and has been suggested to play roles in regulating translation of a subset of mRNAs and in regulating cell cycle progression and cell proliferation...
March 21, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28322269/a-ras-gtpase-associated-protein-is-involved-in-the-phototropic-and-circadian-photobiology-responses-in-fungi
#16
Silvia Polaino, José M Villalobos-Escobedo, Viplendra P S Shakya, Alejandro Miralles-Durán, Suman Chaudhary, Catalina Sanz, Mahdi Shahriari, Eva M Luque, Arturo P Eslava, Luis M Corrochano, Alfredo Herrera-Estrella, Alexander Idnurm
Light is an environmental signal perceived by most eukaryotic organisms and that can have major impacts on their growth and development. The MadC protein in the fungus Phycomyces blakesleeanus (Mucoromycotina) has been postulated to form part of the photosensory input for phototropism of the fruiting body sporangiophores, but the madC gene has remained unidentified since the 1960s when madC mutants were first isolated. In this study the madC gene was identified by positional cloning. All madC mutant strains contain loss-of-function point mutations within a gene predicted to encode a GTPase activating protein (GAP) for Ras...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320828/malaria-epigenetics
#17
Alfred Cortés, Kirk W Deitsch
Organisms with identical genome sequences can show substantial differences in their phenotypes owing to epigenetic changes that result in different use of their genes. Epigenetic regulation of gene expression plays a key role in the control of several fundamental processes in the biology of malaria parasites, including antigenic variation and sexual differentiation. Some of the histone modifications and chromatin-modifying enzymes that control the epigenetic states of malaria genes have been characterized, and their functions are beginning to be unraveled...
March 20, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#18
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28315258/mechanisms-of-iron-sensing-and-regulation-in-the-yeast-saccharomyces-cerevisiae
#19
REVIEW
María Teresa Martínez-Pastor, Ana Perea-García, Sergi Puig
Iron is a redox active element that functions as an essential cofactor in multiple metabolic pathways, including respiration, DNA synthesis and translation. While indispensable for eukaryotic life, excess iron can lead to oxidative damage of macromolecules. Therefore, living organisms have developed sophisticated strategies to optimally regulate iron acquisition, storage and utilization in response to fluctuations in environmental iron bioavailability. In the yeast Saccharomyces cerevisiae, transcription factors Aft1/Aft2 and Yap5 regulate iron metabolism in response to low and high iron levels, respectively...
April 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28306143/mutant-eif2b-leads-to-impaired-mitochondrial-oxidative-phosphorylation-in-vanishing-white-matter-disease
#20
Gali Raini, Reut Sharet, Melisa Herrero, Andrea Atzmon, Anjana Shenoy, Tamar Geiger, Orna Elroy-Stein
Eukaryotic translation initiation factor 2B (eIF2B) is a master regulator of protein synthesis under normal and stress conditions. Mutations in any of the five genes encoding its subunits lead to Vanishing White Matter (VWM) disease, a recessive genetic deadly illness caused by progressive loss of white matter in the brain. In the current study we used fibroblasts, which are not involved in the disease, to demonstrate the involvement of eIF2B in mitochondrial function and abundance. Mass-spectrometry of total proteome of mouse embryonic fibroblasts (MEFs) isolated from Eif2b5(R132H/R132H) mice revealed unbalanced stoichiometry of proteins involved in oxidative phosphorylation and of mitochondrial translation machinery components, among others...
March 17, 2017: Journal of Neurochemistry
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