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Separate transcriptionally regulated pathways specify distinct classes of sister dendrites in a nociceptive neuron.
O'Brien BMJ, Palumbos SD, Novakovic M, Shang X, Sundararajan L, Miller DM
(2017) Dev Biol 432: 248-257
MeSH Terms: Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, DNA-Binding Proteins, Dendrites, Gene Expression Regulation, LIM-Homeodomain Proteins, Membrane Proteins, Nociceptors, Regulatory Elements, Transcriptional, Sensory Receptor Cells, Transcription Factors, Zinc Fingers
Show Abstract · Added March 26, 2019
The dendritic processes of nociceptive neurons transduce external signals into neurochemical cues that alert the organism to potentially damaging stimuli. The receptive field for each sensory neuron is defined by its dendritic arbor, but the mechanisms that shape dendritic architecture are incompletely understood. Using the model nociceptor, the PVD neuron in C. elegans, we determined that two types of PVD lateral branches project along the dorsal/ventral axis to generate the PVD dendritic arbor: (1) Pioneer dendrites that adhere to the epidermis, and (2) Commissural dendrites that fasciculate with circumferential motor neuron processes. Previous reports have shown that the LIM homeodomain transcription factor MEC-3 is required for all higher order PVD branching and that one of its targets, the claudin-like membrane protein HPO-30, preferentially promotes outgrowth of pioneer branches. Here, we show that another MEC-3 target, the conserved TFIIA-like zinc finger transcription factor EGL-46, adopts the alternative role of specifying commissural dendrites. The known EGL-46 binding partner, the TEAD transcription factor EGL-44, is also required for PVD commissural branch outgrowth. Double mutants of hpo-30 and egl-44 show strong enhancement of the lateral branching defect with decreased numbers of both pioneer and commissural dendrites. Thus, HPO-30/Claudin and EGL-46/EGL-44 function downstream of MEC-3 and in parallel acting pathways to direct outgrowth of two distinct classes of PVD dendritic branches.
Copyright © 2017 Elsevier Inc. All rights reserved.
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MeSH Terms
Integrative genomics identifies 7p11.2 as a novel locus for fever and clinical stress response in humans.
Ferguson JF, Meyer NJ, Qu L, Xue C, Liu Y, DerOhannessian SL, Rushefski M, Paschos GK, Tang S, Schadt EE, Li M, Christie JD, Reilly MP
(2015) Hum Mol Genet 24: 1801-12
MeSH Terms: Adolescent, Adult, Aged, Animals, Chromosomes, Human, Pair 7, European Continental Ancestry Group, Female, Fever, Genetic Loci, Genome-Wide Association Study, Humans, Lipopolysaccharides, Male, Mice, Middle Aged, Polymorphism, Single Nucleotide, Regulatory Elements, Transcriptional, Sepsis, Stress, Physiological, Wounds and Injuries, Young Adult
Show Abstract · Added January 20, 2015
Fever predicts clinical outcomes in sepsis, trauma and during cardiovascular stress, yet the genetic determinants are poorly understood. We used an integrative genomics approach to identify novel genomic determinants of the febrile response to experimental endotoxemia. We highlight multiple integrated lines of evidence establishing the clinical relevance of this novel fever locus. Through genome-wide association study (GWAS) of evoked endotoxemia (lipopolysaccharide (LPS) 1 ng/kg IV) in healthy subjects of European ancestry we discovered a locus on chr7p11.2 significantly associated with the peak febrile response to LPS (top single nucleotide polymorphism (SNP) rs7805622, P = 2.4 × 10(-12)), as well as with temperature fluctuation over time. We replicated this association in a smaller independent LPS study (rs7805622, P = 0.03). In clinical translation, this locus was also associated with temperature and mortality in critically ill patients with trauma or severe sepsis. The top GWAS SNPs are not located within protein-coding genes, but have significant cis-expression quantitative trait loci (eQTL) associations with expression of a cluster of genes ∼400 kb upstream, several of which (SUMF2, CCT6A, GBAS) are regulated by LPS in vivo in blood cells. LPS- and cold-treatment of adipose stromal cells in vitro suggest genotype-specific modulation of eQTL candidate genes (PSPH). Several eQTL genes were up-regulated in brown and white adipose following cold exposure in mice, highlighting a potential role in thermogenesis. Thus, through genomic interrogation of experimental endotoxemia, we identified and replicated a novel fever locus on chr7p11.2 that modulates clinical responses in trauma and sepsis, and highlight integrated in vivo and in vitro evidence for possible novel cis candidate genes conserved across human and mouse.
© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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21 MeSH Terms
Acinetobacter baumannii response to host-mediated zinc limitation requires the transcriptional regulator Zur.
Mortensen BL, Rathi S, Chazin WJ, Skaar EP
(2014) J Bacteriol 196: 2616-26
MeSH Terms: Acinetobacter Infections, Acinetobacter baumannii, Animals, Bacterial Proteins, Calgranulin B, Gene Expression Regulation, Bacterial, Liver, Mice, Mice, Inbred C57BL, Mice, Knockout, Mutation, Pneumonia, Bacterial, RNA, Bacterial, Regulatory Elements, Transcriptional, Zinc
Show Abstract · Added May 19, 2014
Acinetobacter baumannii is a leading cause of ventilator-associated pneumonia in intensive care units, and the increasing rates of antibiotic resistance make treating these infections challenging. Consequently, there is an urgent need to develop new antimicrobials to treat A. baumannii infections. One potential therapeutic option is to target bacterial systems involved in maintaining appropriate metal homeostasis, processes that are critical for the growth of pathogens within the host. The A. baumannii inner membrane zinc transporter ZnuABC is required for growth under low-zinc conditions and for A. baumannii pathogenesis. The expression of znuABC is regulated by the transcriptional repressor Zur. To investigate the role of Zur during the A. baumannii response to zinc limitation, a zur deletion mutant was generated, and transcriptional changes were analyzed using RNA sequencing. A number of Zur-regulated genes were identified that exhibit increased expression both when zur is absent and under low-zinc conditions, and Zur binds to predicted Zur box sequences of several genes affected by zinc levels or the zur mutation. Furthermore, the zur mutant is impaired for growth in the presence of both high and low zinc levels compared to wild-type A. baumannii. Finally, the zur mutant exhibits a defect in dissemination in a mouse model of A. baumannii pneumonia, establishing zinc sensing as a critical process during A. baumannii infection. These results define Zur-regulated genes within A. baumannii and demonstrate a requirement for Zur in the A. baumannii response to the various zinc levels experienced within the vertebrate host.
Copyright © 2014, American Society for Microbiology. All Rights Reserved.
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15 MeSH Terms
Phosphorylation-dependent derepression by the response regulator HnoC in the Shewanella oneidensis nitric oxide signaling network.
Plate L, Marletta MA
(2013) Proc Natl Acad Sci U S A 110: E4648-57
MeSH Terms: Bacterial Proteins, Biofilms, DNA Footprinting, Electrophoretic Mobility Shift Assay, Microarray Analysis, Models, Biological, Nitric Oxide, Phosphorylation, Regulatory Elements, Transcriptional, Shewanella, Signal Transduction
Show Abstract · Added March 3, 2020
Nitric oxide (NO) is an important signaling molecule that regulates diverse physiological processes in all domains of life. In many gammaproteobacteria, NO controls behavioral responses through a complex signaling network involving heme-nitric oxide/oxygen binding (H-NOX) domains as selective NO sensors. In Shewanella oneidensis, H-NOX-mediated NO sensing increases biofilm formation, which is thought to serve as a protective mechanism against NO cytotoxicity. The H-NOX/NO-responsive (hno) signaling network involves H-NOX-dependent control of HnoK autophosphorylation and phosphotransfer from HnoK to three response regulators. Two of these response regulators, HnoB and HnoD, regulate cyclic-di-GMP levels and influence biofilm formation. However, the role of the third response regulator in the signaling network, HnoC, has not been determined. Here we describe a role for HnoC as a transcriptional repressor for the signaling genes in the hno network. The genes controlled by HnoC were identified by microarray analysis, and its function as a repressor was confirmed in vivo. HnoC belongs to an uncharacterized family of DNA-binding response regulators. Binding of HnoC to its promoter targets was characterized in vitro, revealing an unprecedented regulation mechanism, which further extends the functional capabilities of DNA-binding response regulators. In the unphosphorylated state HnoC forms a tetramer, which tightly binds to an inverted-repeat target sequence overlapping with the promoter regions. Phosphorylation of HnoC induces dissociation of the response regulator tetramer and detachment of subunits from the promoter DNA, which subsequently leads to transcriptional derepression.
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MeSH Terms
De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.
Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E
(2013) Genome Res 23: 1601-14
MeSH Terms: Animals, B-Lymphocytes, Cell Differentiation, Cell Line, Chromatin, CpG Islands, DNA Methylation, DNA, Intergenic, Enhancer Elements, Genetic, Evolution, Molecular, Female, Gene Expression Profiling, Hematopoietic Stem Cells, High-Throughput Nucleotide Sequencing, Humans, Lymphopoiesis, Pan troglodytes, Phylogeny, Promoter Regions, Genetic, RNA, Untranslated, Regulatory Elements, Transcriptional, Sequence Analysis, DNA, Transcription Initiation, Genetic
Show Abstract · Added February 15, 2016
Deep sequencing of mammalian DNA methylomes has uncovered a previously unpredicted number of discrete hypomethylated regions in intergenic space (iHMRs). Here, we combined whole-genome bisulfite sequencing data with extensive gene expression and chromatin-state data to define functional classes of iHMRs, and to reconstruct the dynamics of their establishment in a developmental setting. Comparing HMR profiles in embryonic stem and primary blood cells, we show that iHMRs mark an exclusive subset of active DNase hypersensitive sites (DHS), and that both developmentally constitutive and cell-type-specific iHMRs display chromatin states typical of distinct regulatory elements. We also observe that iHMR changes are more predictive of nearby gene activity than the promoter HMR itself, and that expression of noncoding RNAs within the iHMR accompanies full activation and complete demethylation of mature B cell enhancers. Conserved sequence features corresponding to iHMR transcript start sites, including a discernible TATA motif, suggest a conserved, functional role for transcription in these regions. Similarly, we explored both primate-specific and human population variation at iHMRs, finding that while enhancer iHMRs are more variable in sequence and methylation status than any other functional class, conservation of the TATA box is highly predictive of iHMR maintenance, reflecting the impact of sequence plasticity and transcriptional signals on iHMR establishment. Overall, our analysis allowed us to construct a three-step timeline in which (1) intergenic DHS are pre-established in the stem cell, (2) partial demethylation of blood-specific intergenic DHSs occurs in blood progenitors, and (3) complete iHMR formation and transcription coincide with enhancer activation in lymphoid-specified cells.
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23 MeSH Terms
Small science: high stakes.
Gamazon ER
(2012) Science 338: 883
MeSH Terms: Genome, Human, Human Genome Project, Humans, Regulatory Elements, Transcriptional
Added April 13, 2017
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4 MeSH Terms
Leishmania-induced repression of selected non-coding RNA genes containing B-box element at their promoters in alternatively polarized M2 macrophages.
Farrow AL, Rana T, Mittal MK, Misra S, Chaudhuri G
(2011) Mol Cell Biochem 350: 47-57
MeSH Terms: Animals, Base Sequence, Cell Polarity, Cells, Cultured, Down-Regulation, Gene Expression Regulation, Humans, Leishmania, Macrophage Activation, Macrophages, Mice, Molecular Sequence Data, Promoter Regions, Genetic, RNA, Small Cytoplasmic, RNA, Untranslated, Regulatory Elements, Transcriptional, Signal Recognition Particle, U937 Cells
Show Abstract · Added July 10, 2015
Leishmania is a group of parasitic protozoa that infect blood and tissue phagocytes including macrophages. We hypothesize that Leishmania is capable of establishing infection inside the macrophages because (a) they infect a subpopulation of macrophages; and (b) they "renovate" the macrophages before the establishment of infection. We found that only alternatively activated polarized M2 macrophages support Leishmania growth. Exposure of M2 macrophages to Leishmania promastigotes represses several selected RNA polymerase III (PolIII)-transcribed non-coding RNA (ncRNA) genes including those of 7SL RNA, vault RNA, and B2 RNA which have B-box element at their promoters. The B-box-binding transcription factor TFIIIC110 is down-regulated in Leishmania-exposed macrophages. Both the surface protease gp63 and the surface glycolipid LPG are required for the down-regulation of the ncRNAs in the M2 macrophages. We conclude that Leishmania surface gp63 collaborates with LPG to down-regulate TFIIIC110 in M2 macrophages to repress B-box containing ncRNA gene promoters.
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18 MeSH Terms
Distal regions of the human IFNG locus direct cell type-specific expression.
Collins PL, Chang S, Henderson M, Soutto M, Davis GM, McLoed AG, Townsend MJ, Glimcher LH, Mortlock DP, Aune TM
(2010) J Immunol 185: 1492-501
MeSH Terms: Animals, Cell Lineage, Cells, Cultured, Conserved Sequence, Core Binding Factor Alpha 3 Subunit, Gene Expression Regulation, Genetic Loci, Humans, Interferon-gamma, Killer Cells, Natural, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Natural Killer T-Cells, Protein Transport, RNA Polymerase II, Regulatory Elements, Transcriptional, Th1 Cells, Transcription Initiation Site
Show Abstract · Added December 10, 2013
Genes, such as IFNG, which are expressed in multiple cell lineages of the immune system, may employ a common set of regulatory elements to direct transcription in multiple cell types or individual regulatory elements to direct expression in individual cell lineages. By employing a bacterial artificial chromosome transgenic system, we demonstrate that IFNG employs unique regulatory elements to achieve lineage-specific transcriptional control. Specifically, a one 1-kb element 30 kb upstream of IFNG activates transcription in T cells and NKT cells but not in NK cells. This distal regulatory element is a Runx3 binding site in Th1 cells and is needed for RNA polymerase II recruitment to IFNG, but it is not absolutely required for histone acetylation of the IFNG locus. These results support a model whereby IFNG uses cis-regulatory elements with cell type-restricted function.
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20 MeSH Terms
Repressive BMP2 gene regulatory elements near the BMP2 promoter.
Jiang S, Chandler RL, Fritz DT, Mortlock DP, Rogers MB
(2010) Biochem Biophys Res Commun 392: 124-8
MeSH Terms: Animals, Base Sequence, Bone Morphogenetic Protein 2, Cell Line, Conserved Sequence, Enhancer Elements, Genetic, Fibroblast Growth Factor 2, GC Rich Sequence, Gene Expression Regulation, Developmental, Genes, Reporter, HeLa Cells, Humans, Mice, Molecular Sequence Data, Osteoblasts, Promoter Regions, Genetic, Regulatory Elements, Transcriptional, Repressor Proteins
Show Abstract · Added June 9, 2010
The level of bone morphogenetic protein 2 (BMP2) profoundly influences essential cell behaviors such as proliferation, differentiation, apoptosis, and migration. The spatial and temporal pattern of BMP2 synthesis, particular in diverse embryonic cells, is highly varied and dynamic. We have identified GC-rich sequences within the BMP2 promoter region that strongly repress gene expression. These elements block the activity of a highly conserved, osteoblast enhancer in response to FGF2 treatment. Both positive and negative gene regulatory elements control BMP2 synthesis. Detecting and mapping the repressive motifs is essential because they impede the identification of developmentally regulated enhancers necessary for normal BMP2 patterns and concentration.
2010 Elsevier Inc. All rights reserved.
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18 MeSH Terms
Control of BMP gene expression by long-range regulatory elements.
Pregizer S, Mortlock DP
(2009) Cytokine Growth Factor Rev 20: 509-15
MeSH Terms: Animals, Animals, Genetically Modified, Bone Development, Bone Morphogenetic Protein 2, Bone Morphogenetic Protein 4, Bone Morphogenetic Protein 5, Bone Morphogenetic Proteins, Gene Expression Regulation, Developmental, Growth Differentiation Factor 6, Humans, Mice, Models, Biological, Regulatory Elements, Transcriptional
Show Abstract · Added September 23, 2013
Much evidence suggests that "developmental regulator" genes, like those encoding transcription factors and signaling molecules, are typically controlled by many modular, tissue-specific cis-regulatory elements that function during embryogenesis. These elements are often far from gene coding regions and promoters. Bone morphogenetic proteins (BMPs) drive many processes in development relating to organogenesis and differentiation. Four BMP family members, Bmp2, Bmp4, Bmp5, and Gdf6, are now known to be under the control of distant cis-regulatory elements. BMPs are thus firmly placed in the category of genes prone to this phenomenon. The analysis of distant BMP regulatory elements has provided insight into the many pleiotropic effects of BMP genes, and underscores the biological importance of non-coding genomic DNA elements.
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13 MeSH Terms