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eukaryotic gene regulation

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https://www.readbyqxmd.com/read/29036702/a-hyperdynamic-h3-3-nucleosome-marks-promoter-regions-in-pluripotent-embryonic-stem-cells
#1
Sharon Schlesinger, Binyamin Kaffe, Shai Melcer, Jose D Aguilera, Divya M Sivaraman, Tommy Kaplan, Eran Meshorer
Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036674/detecting-and-characterizing-micrornas-of-diverse-genomic-origins-via-mirvial
#2
Jing Xia, Lun Li, Tiantian Li, Zhiwei Fang, Kevin Zhang, Junfei Zhou, Hai Peng, Weixiong Zhang
MicroRNAs form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. MicroRNAs may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. We present miRvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs. Extensive results comparing miRvial and six existing microRNA finding methods on six model organisms, Mus musculus, Drosophila melanogaste, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens and Chlamydomonas reinhardtii, demonstrated the utility and rigor of miRvial in detecting novel microRNAs and characterizing features of microRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036355/design-and-implementation-of-a-synthetic-pre-mir-switch-for-controlling-mirna-biogenesis-in-mammals
#3
Janina Atanasov, Florian Groher, Julia E Weigand, Beatrix Suess
Synthetic RNA-based systems have increasingly been used for the regulation of eukaryotic gene expression. Due to their structural properties, riboregulators provide a convenient basis for the development of ligand-dependent controllable systems. Here, we demonstrate reversible conditional control of miRNA biogenesis with an aptamer domain as a sensing unit connected to a natural miRNA precursor for the first time. For the design of the pre-miR switch, we replaced the natural terminal loop with the TetR aptamer...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036326/circular-rnas-are-abundant-and-dynamically-expressed-during-embryonic-muscle-development-in-chickens
#4
Hongjia Ouyang, Xiaolan Chen, Zhijun Wang, Jiao Yu, Xinzheng Jia, Zhenhui Li, Wei Luo, Bahareldin Ali Abdalla, Endashaw Jebessa, Qinghua Nie, Xiquan Zhang
The growth and development of skeletal muscle is regulated by proteins as well as non-coding RNAs. Circular RNAs (circRNAs) are universally expressed in various tissues and cell types, and regulate gene expression in eukaryotes. To identify the circRNAs during chicken embryonic skeletal muscle development, leg muscles of female Xinghua (XH) chicken at three developmental time points 11 embryo age (E11), 16 embryo age (E16) and 1 day post hatch (P1) were performed RNA sequencing. We identified 13,377 circRNAs with 3,036 abundantly expressed and most were derived from coding exons...
October 3, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29035382/regulation-of-heterotrimeric-g-protein-signaling-by-ndpk-nme-proteins-and-caveolins-an-update
#5
Issam H Abu-Taha, Jordi Heijman, Yuxi Feng, Christiane Vettel, Dobromir Dobrev, Thomas Wieland
Heterotrimeric G proteins are pivotal mediators of cellular signal transduction in eukaryotic cells and abnormal G-protein signaling plays an important role in numerous diseases. During the last two decades it has become evident that the activation status of heterotrimeric G proteins is both highly localized and strongly regulated by a number of factors, including a receptor-independent activation pathway of heterotrimeric G proteins that does not involve the classical GDP/GTP exchange and relies on nucleoside diphosphate kinases (NDPKs)...
October 16, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29034140/regulation-of-gene-expression-by-translation-factor-eif5a-hypusine-modified-eif5a-enhances-nonsense-mediated-mrna-decay-in-human-cells
#6
Mainul Hoque, Ji Yeon Park, Yun-Juan Chang, Augusto D Luchessi, Tavane D Cambiaghi, Raghavendra Shamanna, Hartmut M Hanauske-Abel, Bart Holland, Tsafi Pe'ery, Bin Tian, Michael B Mathews
Nonsense-mediated mRNA decay (NMD) couples protein synthesis to mRNA turnover. It eliminates defective transcripts and controls the abundance of certain normal mRNAs. Our study establishes a connection between NMD and the translation factor eIF5A (eukaryotic initiation factor 5A) in human cells. eIF5A modulates the synthesis of groups of proteins (the eIF5A regulon), and undergoes a distinctive two-step post-translational modification (hypusination) catalyzed by deoxyhypusine synthase and deoxyhypusine hydroxylase...
2017: Translation
https://www.readbyqxmd.com/read/29032152/structure-function-characterization-of-the-ell-associated-factor-eaf-from-schizosaccharomyces-pombe
#7
Preeti Dabas, Kumari Sweta, Mary Ekka, Nimisha Sharma
EAF (ELL Associated Factor) proteins interact with the transcription elongation factor, ELL (Eleven nineteen Lysine rich Leukemia) and enhance its ability to stimulate RNA polymerase II-mediated transcriptional elongation in vitro. Schizosaccharomyces pombe contains a single homolog of EAF (SpEAF), which is not essential for survival of S. pombe in contrast to its essential higher eukaryotic homologs. The physiological role of SpEAF is not well understood. In this study, we show that S. pombe EAF is important in regulating growth of S...
October 12, 2017: Gene
https://www.readbyqxmd.com/read/29031807/cytochrome-c-peroxidase-regulates-intracellular-reactive-oxygen-species-and-methylglyoxal-via-enzyme-activities-of-erythroascorbate-peroxidase-and-glutathione-related-enzymes-in-candida-albicans
#8
YoungHo Shin, Sungkyoung Lee, MyungHee Ku, Min-Kyu Kwak, Sa-Ouk Kang
D-erythroascorbate peroxidase (EAPX1) deficiency causes glutathione deprivation, leading to the accumulation of methylglyoxal and reactive oxygen species (ROS), and especially, induction of cytochrome c peroxidase (Ccp1) in Candida albicans. Nevertheless, reciprocal effects between changes in Ccp1 activity and the antioxidative D-erythroascorbic acid- and glutathione-dependent redox status, which reflects methylglyoxal biosynthesis altering pathophysiology are unclear in eukaryotes. To elucidate the effect of CCP1 expression on EAPX1 and glutathione reductase (Glr1) activity-mediated D-erythroascorbic acid biosynthesis and redox homeostasis, the CCP1 gene was disrupted and overexpressed...
October 11, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29031735/the-temporal-expression-profile-of-a-nos3-related-natural-antisense-rna-in-the-brain-suggests-a-possible-role-in-neurogenesis
#9
Gabriela G Chavez, Gabriella Taylor, Jekaterina Garaliene, Guy P Richardson, Sergei A Korneev
Experimental work over the past several years has revealed an unexpected abundance of long natural antisense transcripts (NATs) in eukaryotic species. In light of the proposed role of such RNA molecules in the regulation of gene expression in the brain, attention is now focused on specific examples of neuronal NATs. Of particular interest are NATs that are complementary to mRNAs encoding nitric oxide synthase (NOS), the enzyme responsible for production of the important gaseous neurotransmitter nitric oxide (NO)...
October 12, 2017: Nitric Oxide: Biology and Chemistry
https://www.readbyqxmd.com/read/29020934/transcriptome-analyses-reveal-sr45-to-be-a-neutral-splicing-regulator-and-a-suppressor-of-innate-immunity-in-arabidopsis-thaliana
#10
Xiao-Ning Zhang, Yifei Shi, Jordan J Powers, Nikhil B Gowda, Chong Zhang, Heba M M Ibrahim, Hannah B Ball, Samuel L Chen, Hua Lu, Stephen M Mount
BACKGROUND: Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regulatory proteins and spliceosomal subunits. Although SR45 has orthologs in diverse eukaryotes, including human RNPS1, the sr45-1 null mutant is viable. Narrow flower petals and reduced seed formation suggest that SR45 regulates genes involved in diverse processes, including reproduction...
October 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29019354/iron-sulfur-cluster-biosynthesis-and-trafficking-impact-on-human-disease-conditions
#11
C Wachnowsky, I Fidai, J A Cowan
Iron-sulfur clusters (Fe-S) are one of the most ancient, ubiquitous and versatile classes of metal cofactors found in nature. Proteins that contain Fe-S clusters constitute one of the largest families of proteins, with varied functions that include electron transport, regulation of gene expression, substrate binding and activation, radical generation, and, more recently discovered, DNA repair. Research during the past two decades has shown that mitochondria are central to the biogenesis of Fe-S clusters in eukaryotic cells via a conserved cluster assembly machinery (ISC assembly machinery) that also controls the synthesis of Fe-S clusters of cytosolic and nuclear proteins...
October 11, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29019352/hot-news-gene-therapy-with-crispr-cas9-coming-to-age-for-hiv-cure
#12
Vicente Soriano
The huge success of current antiretroviral therapy is mediated by a triple effect: (i) Halting progression to AIDS in infected persons; (ii) reducing the risk of transmission to contacts (treatment as prevention); and (iii) minimizing the risk of HIV acquisition treating uninfected persons at risk (pre-exposure prophylaxis). However, UNAIDS has estimated that only 70% of infected people globally are diagnosed, only 53% are treated, and overall 44% have undetectable viral load, which is the necessary request for ensuring any antiretroviral benefit...
October 11, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/29018569/deconstructing-a-multiple-antibiotic-resistance-regulation-through-the-quantification-of-its-input-function
#13
Guillermo Rodrigo, Djordje Bajić, Ignacio Elola, Juan F Poyatos
Many essential bacterial responses present complex transcriptional regulation of gene expression. To what extent can the study of these responses substantiate the logic of their regulation? Here, we show how the input function of the genes constituting the response, i.e., the information of how their transcription rates change as function of the signals acting on the regulators, can serve as a quantitative tool to deconstruct the corresponding regulatory logic. To demonstrate this approach, we consider the multiple antibiotic resistance (mar) response in Escherichia coli...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29017967/non-coding-rnas-and-their-roles-in-stress-response-in-plants
#14
REVIEW
Jingjing Wang, Xianwen Meng, Oxana B Dobrovolskaya, Yuriy L Orlov, Ming Chen
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance...
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017848/suppression-of-cotton-leaf-curl-disease-symptoms-in-gossypium-hirsutum-through-over-expression-of-host-encoded-mirnas
#15
Mohd Akmal, Mirza S Baig, Jawaid A Khan
Cotton leaf curl disease (CLCuD), a major factor resulting in the enormous yield losses in cotton crop, is caused by a distinct monopartite begomovirus in association with Cotton leaf curl Multan betasatellite (CLCuMB). Micro(mi)RNAs are known to regulate gene expression in eukaryotes, including antiviral defense in plants. In a previous study, we had computationally identified a set of cotton miRNAs, which were shown to have potential targets in the genomes of Cotton leaf curl Multan virus (CLCuMuV) and CLCuMB at multiple loci...
October 7, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29017815/rna-polymerase-ii-pausing-and-transcriptional-regulation-of-the-hsp70-expression
#16
REVIEW
Heeyoun Bunch
Heat-shock proteins (HSPs) belong to the chaperone protein family whose expression is induced by different stresses including heat-shock. In response to the extracellular or intrinsic stimuli and stresses, HSPs play important roles in the maintenance of cellular homeostasis. HSP70, a major HSP protein (molecular weight, 70 KDa), regulates diverse cellular pathways including protein quality control, translation, immune response, and cancer survival. As a critical cellular defense system to minimize damages from cellular stresses, HSP70 expression and transcriptional activation are rapidly regulated, mainly through the action of a transcription activator, Heat shock factor 1 (HSF1)...
October 3, 2017: European Journal of Cell Biology
https://www.readbyqxmd.com/read/28994762/in-vitro-bioluminescence-assay-to-characterize-circadian-rhythm-in-mammary-epithelial-cells
#17
Mingzhu Fang, Hwan-Goo Kang, Youngil Park, Brian Estrella, Helmut Zarbl
The circadian rhythm is a fundamental physiological process present in all organisms that regulates biological processes ranging from gene expression to sleep behavior. In vertebrates, circadian rhythm is controlled by a molecular oscillator that functions in both the suprachiasmatic nucleus (SCN; central pacemaker) and individual cells comprising most peripheral tissues. More importantly, disruption of circadian rhythm by exposure to light-at-night, environmental stressors and/or toxicants is associated with increased risk of chronic diseases and aging...
September 28, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28993928/tvznf1-is-a-c2h2-zinc-finger-protein-of-trichomonas-vaginalis
#18
José Luis Villalpando, Rodrigo Arreola, Jonathan Puente-Rivera, Elisa Azuara-Liceaga, Jesús Valdés, Lilia López-Canovas, Alma Villalobos-Osnaya, Maria Elizbeth Alvarez-Sánchez
The zinc fingers proteins (ZNF) are the largest family of DNA binding proteins and can act as transcriptional factors in eukaryotes. ZNF are implicated in activation in response to environmental stimulus by biometals such as Zn(2+). Many of these proteins have the classical C2H2 zinc finger motifs (C2H2-ZNFm) of approximately 30 amino acids, where a Zn(2+) ion is coordinated by two cysteine and two histidine residues. Trichomonas vaginalis is a protozoan parasite than responds to environmental changes including Zn(2+)...
October 9, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28991266/macroh2a1-1-regulates-mitochondrial-respiration-by-limiting-nuclear-nad-consumption
#19
Melanija Posavec Marjanović, Sarah Hurtado-Bagès, Maximilian Lassi, Vanesa Valero, Roberto Malinverni, Hélène Delage, Miriam Navarro, David Corujo, Iva Guberovic, Julien Douet, Pau Gama-Perez, Pablo M Garcia-Roves, Ivan Ahel, Andreas G Ladurner, Oscar Yanes, Philippe Bouvet, Mònica Suelves, Raffaele Teperino, J Andrew Pospisilik, Marcus Buschbeck
Histone variants are structural components of eukaryotic chromatin that can replace replication-coupled histones in the nucleosome. The histone variant macroH2A1.1 contains a macrodomain capable of binding NAD(+)-derived metabolites. Here we report that macroH2A1.1 is rapidly induced during myogenic differentiation through a switch in alternative splicing, and that myotubes that lack macroH2A1.1 have a defect in mitochondrial respiratory capacity. We found that the metabolite-binding macrodomain was essential for sustained optimal mitochondrial function but dispensable for gene regulation...
October 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28990488/the-microrna-mir773-is-involved-in-the-arabidopsis-immune-response-to-fungal-pathogens
#20
Raquel Salvador-Guirao, Patricia Baldrich, Detlef Weigel, Ignacio Rubio-Somoza, Blanca San Segundo
MicroRNAs (miRNAs) are 21-24 nucleotide short non-coding RNAs that trigger gene silencing in eukaryotes. In plants, miRNAs play a crucial role in a wide range of developmental processes and adaptive responses to abiotic and biotic stresses. In this work, we investigated the role of miR773 in modulating resistance to infection by fungal pathogens in Arabidopsis thaliana. Interference with miR773 activity by target mimics (in MIM773 plants) and concomitant up-regulation of the miR773 target gene METHYLTRANSFERASE 2 (MET2) increased resistance to infection by necrotrophic (Plectosphaerrella cucumerina) and hemibiotrophic (Fusarium oxysporum, Colletototrichum higginianum) fungal pathogens...
October 9, 2017: Molecular Plant-microbe Interactions: MPMI
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