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Transcriptional regulation

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https://www.readbyqxmd.com/read/27914284/applying-crispr-cas-for-genome-engineering-in-plants-the-best-is-yet-to-come
#1
REVIEW
Holger Puchta
Less than 5 years ago the CRISPR/Cas nuclease was first introduced into eukaryotes, shortly becoming the most efficient and widely used tool for genome engineering. For plants, efforts were centred on obtaining heritable changes in most transformable crop species by inducing mutations into open reading frames of interest, via non-homologous end joining. Now it is important to take the next steps and further develop the technology to reach its full potential. For breeding, besides using DNA-free editing and avoiding off target effects, it will be desirable to apply the system for the mutation of regulatory elements and for more complex genome rearrangements...
November 30, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27914205/mitochondrial-genotype-and-phenotypic-plasticity-of-gene-expression-in-response-to-cold-acclimation-in-killifish
#2
Timothy M Healy, Heather J Bryant, Patricia M Schulte
Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes...
December 3, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27914036/prolactin-regulatory-element-binding-protein-is-involved-in-suppression-of-the-adiponectin-gene-in-vivo
#3
X Z Zhang, H Imachi, J Y Lyu, K Fukunaga, S Sato, T Ibata, T Kobayashi, T Yoshimoto, F Kikuchi, T Dong, K Murao
PURPOSE: Prolactin regulatory element-binding protein (PREB), a member of the WD-repeat protein family, has been recognized as a transcriptional factor that regulates prolactin promoter activity in the anterior pituitary of rats. PREB is expressed not only in the pituitary but also in various other tissues, including the adipose tissue. Previous studies have shown that PREB acts as a transcriptional regulator and suppresses the expression of the adiponectin gene in cultured 3T3L1 preadipocytes...
December 2, 2016: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/27914009/serum-response-factor-srf-ablation-interferes-with-acute-stress-associated-immediate-and-long-term-coping-mechanisms
#4
Annemarie Zimprich, Gabi Mroz, Christopher Meyer Zu Reckendorf, Sofia Anastasiadou, Philip Förstner, Lillian Garrett, Sabine M Hölter, Lore Becker, Jan Rozman, Cornelia Prehn, Birgit Rathkolb, Kristin Moreth, Wolfgang Wurst, Thomas Klopstock, Martin Klingenspor, Jerzy Adamski, Eckhard Wolf, Raffi Bekeredjian, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabe de Angelis, Bernd Knöll
Stress experience modulates behavior, metabolism, and energy expenditure of organisms. One molecular hallmark of an acute stress response is a rapid induction of immediate early genes (IEGs) such as c-Fos and Egr family members. IEG transcription in neurons is mediated by the neuronal activity-driven gene regulator serum response factor (SRF). We show a first role of SRF in immediate and long-lasting acute restraint stress (AS) responses. For this, we employed a standardized mouse phenotyping protocol at the German Mouse Clinic (GMC) including behavioral, metabolic, and cardiologic tests as well as gene expression profiling to analyze the consequences of forebrain-specific SRF deletion in mice exposed to AS...
December 2, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27913791/circadian-transcription-factor-bmal1-regulates-innate-immunity-against-select-rna-viruses
#5
Tanmay Majumdar, Jayeeta Dhar, Sonal Patel, Roman Kondratov, Sailen Barik
BMAL1 (brain and muscle ARNT-like protein 1, also known as MOP3 or ARNT3) belongs to the family of the basic helix-loop-helix (bHLH)-PAS domain-containing transcription factors, and is a key component of the molecular oscillator that generates circadian rhythms. Here, we report that BMAL1-deficient cells are significantly more susceptible to infection by two major respiratory viruses of the Paramyxoviridae family, namely RSV and PIV3. Embryonic fibroblasts from Bmal1(-/-) mice produced nearly 10-fold more progeny virus than their wild type controls...
December 1, 2016: Innate Immunity
https://www.readbyqxmd.com/read/27913726/competitive-binding-between-seryl-trna-synthetase-yy1-complex-and-nfkb1-at-the-distal-segment-results-in-differential-regulation-of-human-vegfa-promoter-activity-during-angiogenesis
#6
Chuan-Yang Fu, Po-Chun Wang, Huai-Jen Tsai
Vascular endothelial growth factor (VEGF) plays a pivotal role in angiogenesis. Previous studies focused on transcriptional regulation modulated by proximal upstream cis-regulatory elements (CREs) of the human vegfa promoter. However, we hypothesized that distal upstream CREs may also be involved in controlling vegfa transcription. In this study, we found that the catalytic domain of Seryl-tRNA synthetase (SerRS) interacted with transcription factor Yin Yang 1 (YY1) to form a SerRS/YY1 complex that negatively controls vegfa promoter activity through binding distal CREs at -4654 to -4623 of vegfa Particularly, we demonstrated that the -4654 to -4623 segment, which predominantly controls vegfa promoter activity, is involved in competitive binding between SerRS/YY1 complex and NFKB1...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913706/stat1-promotes-kras-colon-tumor-growth-and-susceptibility-to-pharmacological-inhibition-of-translation-initiation-factor-eif4a
#7
Shuo Wang, Cedric Darini, Laurent Désaubry, Antonis E Koromilas
The transcription factor STAT1 displays antitumor functions for certain forms of cancer via immunoregulatory and cell-autonomous pathways. Paradoxically, STAT1 can promote the survival of different tumor types treated with chemotherapeutic drugs through mechanisms that are not clearly defined. Herein, we demonstrate that STAT1 displays prosurvival effects in human KRAS colon tumor cells by regulating pathways that converge on the initiation of mRNA translation. Specifically, STAT1 increases PI3K class IB signaling and promotes the downregulation of the programmed cell death protein 4 (PDCD4), a protein with tumor-suppressive properties...
December 2016: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/27913676/translational-control-by-mtor-independent-routes-how-eif6-organizes-metabolism
#8
REVIEW
Annarita Miluzio, Sara Ricciardi, Nicola Manfrini, Roberta Alfieri, Stefania Oliveto, Daniela Brina, Stefano Biffo
Over the past few years, there has been a growing interest in the interconnection between translation and metabolism. Important oncogenic pathways, like those elicited by c-Myc transcription factor and mTOR kinase, couple the activation of the translational machinery with glycolysis and fatty acid synthesis. Eukaryotic initiation factor 6 (eIF6) is a factor necessary for 60S ribosome maturation. eIF6 acts also as a cytoplasmic translation initiation factor, downstream of growth factor stimulation. eIF6 is up-regulated in several tumor types...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913661/effects-of-exendin-4-on-the-intrarenal-renin-angiotensin-system-and-interstitial-fibrosis-in-unilateral-ureteral-obstruction-mice-exendin-4-and-unilateral-ureteral-obstruction
#9
Ying Le, Zongji Zheng, Junyu Xue, Mengling Cheng, Meiping Guan, Yaoming Xue
OBJECTIVE: The objective of this article is to investigate the renoprotecive effects of exendin-4 in a mouse model of unilateral ureteral obstruction (UUO) and explore the putative mechanisms. METHODS: Male Balbc mice underwent sham operation or UUO surgery, and then received intraperitoneal injection of vehicle or exendin-4, respectively. After 14 days, mice were sacrificed and the left kidneys were collected and analyzed by histology, immunohistochemistry, Western blot, quantitative real-time reverse transcription polymerase chain reaction, radioimmunoassay and enzyme-linked immunosorbent assay...
October 2016: Journal of the Renin-angiotensin-aldosterone System: JRAAS
https://www.readbyqxmd.com/read/27913648/cd36-mediated-uptake-of-surfactant-lipids-by-human-macrophages-promotes-intracellular-growth-of-mycobacterium-tuberculosis
#10
Claire E Dodd, Charlie J Pyle, Rebecca Glowinski, Murugesan V S Rajaram, Larry S Schlesinger
Mycobacterium tuberculosis imposes a large global health burden as the airborne agent of tuberculosis. Mycobacterium tuberculosis has been flourishing in human populations for millennia and is therefore highly adapted to the lung environment. Alveolar macrophages, a major host cell niche for M. tuberculosis, are not only phagocytose inhaled microbes and particulate matter but are also crucial in catabolizing lung surfactant, a lipid-protein complex that lines the alveolar spaces. Because macrophage host defense properties can be regulated by surfactant and M...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27913643/biogenesis-and-transcriptional-regulation-of-long-noncoding-rnas-in-the-human-immune-system
#11
REVIEW
Charles F Spurlock, Philip S Crooke, Thomas M Aune
The central dogma of molecular biology states that DNA makes RNA makes protein. Discoveries over the last quarter of a century found that the process of DNA transcription into RNA gives rise to a diverse array of functional RNA species, including genes that code for protein and noncoding RNAs. For decades, the focus has been on understanding how protein-coding genes are regulated to influence protein expression. However, with the completion of the Human Genome Project and follow-up ENCODE data, it is now appreciated that only 2-3% of the genome codes for protein-coding gene exons and that the bulk of the transcribed genome, apart from ribosomal RNAs, is at the level of noncoding RNA genes...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27913641/translation-repression-by-maternal-rna-binding-protein-zar1-is-essential-for-early-oogenesis-in-zebrafish
#12
Liyun Miao, Yue Yuan, Feng Cheng, Junshun Fang, Fang Zhou, Weirui Ma, Yan Jiang, Xiahe Huang, Yingchun Wang, Lingjuan Shan, Dahua Chen, Jian Zhang
Large numbers of maternal RNAs are deposited in oocytes and are reserved for later development. Control of maternal RNA translation during oocyte maturation has been extensively investigated and its regulatory mechanisms are well documented. However, translational regulation of maternal RNAs in early oogenesis is largely unexplored. In this study, we generated zebrafish zar1 mutants which result in early oocyte apoptosis and fully penetrant male development. Loss of p53 suppresses the apoptosis in zar1 mutants and restores oocyte development...
December 2, 2016: Development
https://www.readbyqxmd.com/read/27913638/ms23-a-master-basic-helix-loop-helix-factor-regulates-the-specification-and-development-of-tapetum-in-maize
#13
Guo-Ling Nan, Jixian Zhai, Siwaret Arikit, Darren Morrow, John Fernandes, Lan Mai, Nhi Nguyen, Blake C Meyers, Virginia Walbot
Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed...
December 2, 2016: Development
https://www.readbyqxmd.com/read/27913634/comparative-analysis-highlights-variable-genome-content-of-wheat-rusts-and-divergence-of-the-mating-loci
#14
Christina A Cuomo, Guus Bakkeren, Hala Badr Khalil, Vinay Panwar, David Joly, Rob Linning, Sharadha Sakthikumar, Xiao Song, Xian Adiconis, Lin Fan, Jonathan M Goldberg, Joshua Z Levin, Sarah Young, Qiandong Zeng, Yehoshua Anikster, Myron Bruce, Meinan Wang, Chuntao Yin, Brent McCallum, Les J Szabo, Scot Hulbert, Xiaming Chen, John P Fellers
Three members of the Puccinia genus, P. triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi and basidiomycetes, and to identify genes of significance for infection...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27913621/identification-of-hepatic-lysophosphatidylcholine-acyltransferase-3-as-a-novel-target-gene-regulated-by-peroxisome-proliferator-activated-receptor-%C3%AE
#15
Amar Bahadur Singh, Jingwen Liu
Peroxisome proliferator-activated receptor δ (PPARδ) regulates many genes involved in lipid metabolism. Hepatic lysophosphatidylcholine acyltransferase 3 (LPCAT3) has critical functions in triglycerides transport and ER stress response due to its unique ability to catalyze the incorporation of polyunsaturated fatty acids into phospholipids. Previous studies identified liver X receptor as the transcription factor controlling LPCAT3 expression in mouse liver tissue. Here we show that the hepatic LPCAT3 gene is transcriptionally regulated by PPARδ...
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27913604/conversion-of-t-cells-to-b-cells-by-inactivation-of-polycomb-mediated-epigenetic-suppression-of-the-b-lineage-program
#16
Tomokatsu Ikawa, Kyoko Masuda, Takaho A Endo, Mitsuhiro Endo, Kyoichi Isono, Yoko Koseki, Rinako Nakagawa, Kohei Kometani, Junichiro Takano, Yasutoshi Agata, Yoshimoto Katsura, Tomohiro Kurosaki, Miguel Vidal, Haruhiko Koseki, Hiroshi Kawamoto
In general, cell fate is determined primarily by transcription factors, followed by epigenetic mechanisms fixing the status. While the importance of transcription factors controlling cell fate has been well characterized, epigenetic regulation of cell fate maintenance remains to be elucidated. Here we provide an obvious fate conversion case, in which the inactivation of polycomb-medicated epigenetic regulation results in conversion of T-lineage progenitors to the B-cell fate. In T-cell-specific Ring1A/B-deficient mice, T-cell development was severely blocked at an immature stage...
December 2, 2016: Genes & Development
https://www.readbyqxmd.com/read/27913603/the-tumor-suppressor-flcn-mediates-an-alternate-mtor-pathway-to-regulate-browning-of-adipose-tissue
#17
Shogo Wada, Michael Neinast, Cholsoon Jang, Yasir H Ibrahim, Gina Lee, Apoorva Babu, Jian Li, Atsushi Hoshino, Glenn C Rowe, James Rhee, José A Martina, Rosa Puertollano, John Blenis, Michael Morley, Joseph A Baur, Patrick Seale, Zoltan Arany
Noncanonical mechanistic target of rapamycin (mTOR) pathways remain poorly understood. Mutations in the tumor suppressor folliculin (FLCN) cause Birt-Hogg-Dubé syndrome, a hamartomatous disease marked by mitochondria-rich kidney tumors. FLCN functionally interacts with mTOR and is expressed in most tissues, but its role in fat has not been explored. We show here that FLCN regulates adipose tissue browning via mTOR and the transcription factor TFE3. Adipose-specific deletion of FLCN relieves mTOR-dependent cytoplasmic retention of TFE3, leading to direct induction of the PGC-1 transcriptional coactivators, drivers of mitochondrial biogenesis and the browning program...
December 2, 2016: Genes & Development
https://www.readbyqxmd.com/read/27913583/epigenetic-control-of-microsomal-prostaglandin-e-synthase-1-by-hdac-mediated-recruitment-of-p300
#18
Christian Fork, Andrea E Vasconez, Patrick Janetzko, Carlo Angioni, Yannick Schreiber, Nerea Ferreiros, Gerd Geisslinger, Matthias S Leisegang, Dieter Steinhilber, Ralf P Brandes
: Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most widely used medicine to treat pain, fever, inflammation and to inhibit platelet function. Understanding the expression regulation of enzymes of the prostanoid pathway is of great medical relevance. Histone acetylation crucially controls gene expression. We set out to identify the impact of histone deacetylases (HDACs) on the generation of prostanoids and examine the consequences on vascular function. Inhibition of HDACs (HDACi) with the pan HDAC inhibitor SAHA attenuated prostaglandin E2 (PGE2) generation in the murine vasculature and in human vascular smooth muscle cells...
December 2, 2016: Journal of Lipid Research
https://www.readbyqxmd.com/read/27913570/revisiting-the-human-polypeptide-galnac-t1-and-t13-paralogs
#19
María Florencia Festari, Felipe Trajtenberg, Nora Berois, Sergio Pantano, Leslie Revoredo, Yun Kong, Patricia Solari-Saquieres, Yoshiki Narimatsu, Teresa Freire, Sylvie Bay, Carlos Robello, Jean Bénard, Thomas A Gerken, Henrik Clausen, Eduardo Osinaga
Polypeptide GalNAc-transferases (GalNAc-Ts) constitute a family of 20 human glycosyltransferases (comprising 9 subfamilies), which initiate mucin-type O-glycosylation. The O-glycoproteome is thought to be differentially regulated via the different substrate specificities and expression patterns of each GalNAc-T isoforms. Here, we present a comprehensive in vitro analysis of the peptide substrate specificity of GalNAc-T13, showing that it essentially overlaps with the ubiquitous expressed GalNAc-T1 isoform found in the same subfamily as T13...
November 22, 2016: Glycobiology
https://www.readbyqxmd.com/read/27913566/th2-responses-are-primed-by-skin-dendritic-cells-with-distinct-transcriptional-profiles
#20
Lisa M Connor, Shiau-Choot Tang, Emmanuelle Cognard, Sotaro Ochiai, Kerry L Hilligan, Samuel I Old, Christophe Pellefigues, Ruby F White, Deepa Patel, Adam Alexander T Smith, David A Eccles, Olivier Lamiable, Melanie J McConnell, Franca Ronchese
The dendritic cell signals required for the in vivo priming of IL-4-producing T cells are unknown. We used RNA sequencing to characterize DCs from skin LN of mice exposed to two different Th2 stimuli: the helminth parasite Nippostrongylus brasiliensis (Nb) and the contact sensitizer dibutyl phthalate (DBP)-FITC. Both Nb and DBP-FITC induced extensive transcriptional changes that involved multiple DC subsets. Surprisingly, these transcriptional changes were highly distinct in the two models, with only a small number of genes being similarly regulated in both conditions...
December 2, 2016: Journal of Experimental Medicine
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