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gene regulation in eukaryotes

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https://www.readbyqxmd.com/read/29772845/doxycycline-impairs-mitochondrial-function-and-protects-human-glioma-cells-from-hypoxia-induced-cell-death-implications-of-using-tet-inducible-systems
#1
Anna-Luisa Luger, Benedikt Sauer, Nadja I Lorenz, Anna L Engel, Yannick Braun, Martin Voss, Patrick N Harter, Joachim P Steinbach, Michael W Ronellenfitsch
Inducible gene expression is an important tool in molecular biology research to study protein function. Most frequently, the antibiotic doxycycline is used for regulation of so-called tetracycline (Tet)-inducible systems. In contrast to stable gene overexpression, these systems allow investigation of acute and reversible effects of cellular protein induction. Recent reports have already called for caution when using Tet-inducible systems as the employed antibiotics can disturb mitochondrial function and alter cellular metabolism by interfering with mitochondrial translation...
May 17, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29772251/advances-of-dnase-seq-for-mapping-active-gene-regulatory-elements-across-the-genome-in-animals
#2
REVIEW
Ailing Chen, Daozhen Chen, Ying Chen
Expression of the eukaryotic genome is a highly complex and tightly regulated process, and its regulation depends on interactions among cis-acting elements and transcription factors. Identification of active gene regulatory elements is key to understanding transcriptional control of biological processes including differentiation, development, proliferation, cell-type specificity, and responses to the environment. DNase I hypersensitive sites (DHSs) are markers of open chromatin that provide a very effective method of targeting all types of cis-regulatory elements (CREs) including enhancers, promoters, insulators, silencers, and locus control regions...
May 14, 2018: Gene
https://www.readbyqxmd.com/read/29769310/tumor-associated-intronic-editing-of-hnrpll-generates-a-novel-splicing-variant-linked-to-cell-proliferation
#3
Yi-Tung Chen, Ian Yi-Feng Chang, Hsuan Liu, Chung-Pei Ma, Yu-Ping Kuo, Chieh-Tien Shih, Ying-Hsin Shih, Lin Kang, Bertrand Chin-Ming Tan
Processing of the eukaryotic transcriptome is a dynamic regulatory mechanism that confers genetic diversity, and splicing and A-to-I RNA editing are well-characterized examples of such processing. Growing evidence reveals the crosstalk between the splicing and RNA editing, but there is a paucity of substantial evidence for its mechanistic details and contribution in a physiological context. Here, our findings demonstrate that tumor-associated differential RNA editing, in conjunction with splicing machinery, regulates the expression of variants of HNRPLL, a gene encoding splicing factor...
May 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29758131/the-outer-membrane-omp85-like-protein-p39-influences-metabolic-homeostasis-in-mature-arabidopsis-thaliana
#4
Yi-Ching Hsueh, Kerstin Nicolaisen, Lucia E Gross, Joachim Nöthen, Nicolas Schauer, Lea Vojta, Franziska Ertel, Ina Koch, Roman Ladig, Hrvoje Fulgosi, Alisdair R Fernie, Enrico Schleiff
Omp85 proteins form a large membrane protein family found in bacteria and eukaryotes. Omp85 proteins are composed of a C-terminal β-barrel-shaped membrane domain and one, or more, N-terminal polypeptide-transport-associated (POTRA) domain(s). However, Arabidopsis thaliana contains two genes coding for Omp85 proteins without POTRA domain. One gene is designated P39, according to the molecular weight of the encoded protein. The protein is targeted to plastids and it was established that p39 shows electrophysiological properties similar to the other Omp85 family members, particularly to the one designated Toc75V/Oep80...
May 14, 2018: Plant Biology
https://www.readbyqxmd.com/read/29755419/the-fusarium-graminearum-histone-acetyltransferases-are-important-for-morphogenesis-don-biosynthesis-and-pathogenicity
#5
Xiangjiu Kong, Anne D van Diepeningen, Theo A J van der Lee, Cees Waalwijk, Jingsheng Xu, Jin Xu, Hao Zhang, Wanquan Chen, Jie Feng
Post-translational modifications of chromatin structure by histone acetyltransferase (HATs) play a central role in the regulation of gene expression and various biological processes in eukaryotes. Although HAT genes have been studied in many fungi, few of them have been functionally characterized. In this study, we identified and characterized four putative HATs ( FgGCN5, FgRTT109, FgSAS2, FgSAS3 ) in the plant pathogenic ascomycete Fusarium graminearum , the causal agent of Fusarium head blight of wheat and barley...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29754246/a-rapid-combinatorial-approach-to-assembling-synthetic-prokaryotic-and-eukaryotic-protein-expression-vectors
#6
Rebecca Mullinax, Sarah E Johns, Denise Rhodes, Vivian Zhang, Nancy McKinney, Katherine A Felts, Carsten P Carstens, Peter Sheffield
Vector construction and gene cloning are ubiquitous techniques essential to all fields of biological and medical research. They are the first steps in many endeavors leading to expressing proteins to understand gene function and regulation. However, they can often be rate-limiting, particularly in multi-gene studies, due to the time and effort required to assemble gene constructs and to identify the optimal constructs for protein expression.The SureVector system was developed to address this by enabling the rapid and reliable assembly of multiple DNA modules into a recombinant plasmid containing a gene-of-interest (GOI)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29754146/transcriptional-e2f1-2-5-8-as-potential-targets-and-transcriptional-e2f3-6-7-as-new-biomarkers-for-the-prognosis-of-human-lung-carcinoma
#7
Cheng-Cao Sun, Qun Zhou, Wei Hu, Shu-Jun Li, Feng Zhang, Zhen-Long Chen, Guang Li, Zhuo-Yue Bi, Yong-Yi Bi, Feng-Yun Gong, Tao Bo, Zhan-Peng Yuan, Wei-Dong Hu, Bo-Tao Zhan, Qian Zhang, Qi-Zhu Tang, De-Jia Li
E2F is a group of genes that encode a family of transcription factors (TFs) in higher eukaryotes and participate in cell cycle regulation and DNA synthesis in mammalian cells. Evidence from cell lines, mouse models, and human tissues indicates that TFs are implicated in lung cancer (LC) tumorigenesis. However, the diverse expression patterns and prognostic values of eight E2Fs have yet to be elucidated. In the current study, we examined the transcriptional and survival data of E2Fs in patients with LC from ONCOMINE, GEPIA, Kaplan-Meier Plotter, and cBioPortal databases...
May 11, 2018: Aging
https://www.readbyqxmd.com/read/29752751/intact-arabidopsis-rpb1-functions-in-stem-cell-niches-maintenance-and-cell-cycling-control
#8
Qian-Qian Zhang, Li Ying, Zhao-Ying Fu, Xun-Biao Liu, Kai Yuan, Ying Fang, Yan Liu, Gang Li, Xian-Sheng Zhang, Kang Chong, Lei Ge
Plant meristem activity depends on accurate execution of transcriptional networks required for establishing optimum functioning of stem cell niches. An Arabidopsis mutant card1-1 (constitutive auxin response with DR5:GFP) that encodes a truncated RPB1 (RNA Polymerase II's largest subunit) with shortened C-terminal domain (CTD) was identified. Phosphorylation of the CTD repeats of RPB1 is coupled to transcription in eukaryotes. Here we uncover that the truncated CTD of RPB1 disturbed cell cycling and enlarged the size of shoot and root meristem...
May 12, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29752696/total-saponins-of-rubus-parvifolius-l-exhibited-anti-leukemia-effect-in-vivo-through-stat3-and-eif4e-signaling-pathways
#9
Xiao-Feng Xu, Ru-Bin Cheng, Xue-Jin Zhang, Rui-Lan Gao
OBJECTIVE: To investigate the anti-leukemia effect of total saponins of Rubus parvifolius L. (TSRP) on K562 cell xenografts in nude mice and the mechanisms of action. METHODS: The K562 cell xenografts in nude mice were established, and then randomly divided into 5 groups, the control group, the cytosine arabinoside group(Ara-c) and 3 TSRP groups (20, 40 and 100 mg/kg). The tumor volume and mass of each group of nude mice were measured and the anti-tumor rates of TSRP were calculated subsequently...
May 11, 2018: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/29746549/circularly-permuted-variants-of-two-cg-specific-prokaryotic-dna-methyltransferases
#10
Pál Albert, Bence Varga, Nikolett Zsibrita, Antal Kiss
The highly similar prokaryotic DNA (cytosine-5) methyltransferases (C5-MTases) M.MpeI and M.SssI share the specificity of eukaryotic C5-MTases (5'-CG), and can be useful research tools in the study of eukaryotic DNA methylation and epigenetic regulation. In an effort to improve the stability and solubility of complementing fragments of the two MTases, genes encoding circularly permuted (CP) variants of M.MpeI and M.SssI were created, and cloned in a plasmid vector downstream of an arabinose-inducible promoter...
2018: PloS One
https://www.readbyqxmd.com/read/29744037/endoplasmic-reticulum-turnover-er-phagy-and-other-flavors-in-selective-and-non-selective-er-clearance
#11
REVIEW
Ilaria Fregno, Maurizio Molinari
The endoplasmic reticulum (ER) is a highly dynamic organelle in eukaryotic cells. It is deputed to lipid and protein biosynthesis, calcium storage, and the detoxification of various exogenous and endogenous harmful compounds. ER activity and size must be adapted rapidly to environmental and developmental conditions or biosynthetic demand. This is achieved on induction of thoroughly studied transcriptional/translational programs defined as "unfolded protein responses" that increase the ER volume and the expression of ER-resident proteins regulating the numerous ER functions...
2018: F1000Research
https://www.readbyqxmd.com/read/29740415/d-serine-metabolism-and-its-importance-in-development-of-dictyostelium-discoideum
#12
Tomokazu Ito, Natsuki Hamauchi, Taisuke Hagi, Naoya Morohashi, Hisashi Hemmi, Yukie G Sato, Tamao Saito, Tohru Yoshimura
In mammals, D-Ser is synthesized by serine racemase (SR) and degraded by D-amino acid oxidase (DAO). D-Ser acts as an endogenous ligand for N -methyl-D-aspartate (NMDA)- and δ2 glutamate receptors, and is involved in brain functions such as learning and memory. Although SR homologs are highly conserved in eukaryotes, little is known about the significance of D-Ser in non-mammals. In contrast to mammals, the slime mold Dictyostelium discoideum genome encodes SR, DAO, and additionally D-Ser specific degradation enzyme D-Ser dehydratase (DSD), but not NMDA- and δ2 glutamate receptors...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29739859/the-makings-of-the-actin-code-regulation-of-actin-s-biological-function-at-the-amino-acid-and-nucleotide-level
#13
REVIEW
Pavan Vedula, Anna Kashina
The actin cytoskeleton plays key roles in every eukaryotic cell and is essential for cell adhesion, migration, mechanosensing, and contractility in muscle and non-muscle tissues. In higher vertebrates, from birds through to mammals, actin is represented by a family of six conserved genes. Although these genes have evolved independently for more than 100 million years, they encode proteins with ≥94% sequence identity, which are differentially expressed in different tissues, and tightly regulated throughout embryogenesis and adulthood...
May 8, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29739806/the-surveillance-of-pre-mrna-splicing-is-an-early-step-in-c-elegans-rnai-of-endogenous-genes
#14
Martin A Newman, Fei Ji, Sylvia E J Fischer, Anthony Anselmo, Ruslan I Sadreyev, Gary Ruvkun
RNAi pathways detect and silence foreign nucleic acids such as viruses as well as endogenous genes in many species. The phylogenetic profile across eukaryotes of proteins that mediate key steps in RNAi is correlated with the profiles of multiple mRNA splicing proteins and with intron number, suggesting that RNAi may surveil mRNA splicing to detect the divergent or absent introns of viruses. Here we examine the role of mRNA splicing in Caenorhabditis elegans RNAi . We found that viable null mutations in U1 and U2 small nuclear ribonucleic protein (snRNP)-specific splicing factor genes cause defects in RNAi...
May 8, 2018: Genes & Development
https://www.readbyqxmd.com/read/29738831/histone-variant-h2a-z-antagonizes-the-positive-effect-of-the-transcriptional-activator-cpc1-to-regulate-catalase-3-expression-under-normal-and-oxidative-stress-conditions
#15
Qing Dong, Yajun Wang, Shaohua Qi, Kexin Gai, Qun He, Ying Wang
In eukaryotes, deposition of the histone variant H2A.Z into nucleosomes through the chromatin remodeling complex, SWR1, is a crucial step in modulating gene transcription. Recently, H2A.Z has been shown to control the expression of responsive genes, but the underlying mechanism of how H2A.Z responds to physiological stimuli is not well understood. Here, we reveal that, in Neurospora crassa, H2A.Z is a negative regulator of catalase-3 gene, which is responsible for resistance to oxidative stress. H2A.Z represses cat-3 gene expression through direct incorporation at cat-3 locus in a SWR1 complex dependent pathway...
May 5, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29738749/the-vaginal-eukaryotic-dna-virome-and-preterm-birth
#16
Kristine M Wylie, Todd N Wylie, Alison G Cahill, George A Macones, Methodius G Tuuli, Molly J Stout
BACKGROUND: Despite decades of attempts to link infectious agents to preterm birth, an exact causative microbe or community of microbes remains elusive. Culture-independent sequencing of vaginal bacterial communities demonstrates community characteristics are associated with preterm birth, although none are specific enough to apply clinically. Viruses are important components of the vaginal microbiome and have dynamic relationships with vaginal bacterial communities. We hypothesized that vaginal eukaryotic DNA viral communities (the "vaginal virome") either alone or in the context of bacterial communities are associated with preterm birth...
May 5, 2018: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29738683/argonaute-proteins-and-mechanisms-of-rna-interference-in-eukaryotes-and-prokaryotes
#17
REVIEW
A V Olina, A V Kulbachinskiy, A A Aravin, D M Esyunina
Noncoding RNAs play essential roles in genetic regulation in all organisms. In eukaryotic cells, many small noncoding RNAs act in complex with Argonaute proteins and regulate gene expression by recognizing complementary RNA targets. The complexes of Argonaute proteins with small RNAs also play a key role in silencing of mobile genetic elements and, in some cases, viruses. These processes are collectively called RNA interference. RNA interference is a powerful tool for specific gene silencing in both basic research and therapeutic applications...
May 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29735745/control-of-mitotic-chromosome-condensation-by-the-fission-yeast-transcription-factor-zas1
#18
Christoph Schiklenk, Boryana Petrova, Marc Kschonsak, Markus Hassler, Carlo Klein, Toby J Gibson, Christian H Haering
Although the formation of rod-shaped chromosomes is vital for the correct segregation of eukaryotic genomes during cell divisions, the molecular mechanisms that control the chromosome condensation process have remained largely unknown. Here, we identify the C2 H2 zinc-finger transcription factor Zas1 as a key regulator of mitotic condensation dynamics in a quantitative live-cell microscopy screen of the fission yeast Schizosaccharomyces pombe By binding to specific DNA target sequences in their promoter regions, Zas1 controls expression of the Cnd1 subunit of the condensin protein complex and several other target genes, whose combined misregulation in zas1 mutants results in defects in chromosome condensation and segregation...
May 7, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29734756/translation-control-by-p53
#19
Justina Kasteri, Dibash Das, Xuelin Zhong, Leah Persaud, Ashleigh Francis, Hilal Muharam, Moira Sauane
The translation of mRNAs plays a critical role in the regulation of gene expression and therefore, in the regulation of cell proliferation, differentiation and apoptosis. Unrestricted initiation of translation causes malignant transformation and plays a key role in the maintenance and progression of cancers. Translation initiation is regulated by the ternary complex and the eukaryotic initiation factor 4F (eIF4F) complex. The p53 tumor suppressor protein is the most well studied mammalian transcription factor that mediates a variety of anti-proliferative processes...
May 5, 2018: Cancers
https://www.readbyqxmd.com/read/29734115/transcriptional-and-posttranscriptional-repression-of-histone-deacetylases-by-docosahexaenoic-acid-in-macrophages
#20
Tho X Pham, Minkyung Bae, Yoojin Lee, Young-Ki Park, Ji-Young Lee
Histone deacetylation is one of the posttranslational modifications of histones by which eukaryotic cells alter gene transcription. Although fatty acids are the best known macronutrients that modulate gene expression in inflammatory pathways, it is unclear whether common fatty acids in diets can regulate the expression of histone deacetylases (HDACs) in macrophages. We determined the effects of fatty acids, including palmitic acid (PA), oleic acid (OA), linoleic acid, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), on the expression of HDAC isoforms in RAW 264...
March 10, 2018: Journal of Nutritional Biochemistry
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