Mapping of hns sites in Typhimurium 14028 using a tiling oligo array
Ontology highlight
ABSTRACT:
ORGANISM(S): Salmonella
SUBMITTER: Henry Rosen
PROVIDER: E-GEOD-4879 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella.
Navarre William Wiley WW Porwollik Steffen S Wang Yipeng Y McClelland Michael M Rosen Henry H Libby Stephen J SJ Fang Ferric C FC
Science (New York, N.Y.) 20060608 5784
Horizontal gene transfer plays a major role in microbial evolution. However, newly acquired sequences can decrease fitness unless integrated into preexisting regulatory networks. We found that the histone-like nucleoid structuring protein (H-NS) selectively silences horizontally acquired genes by targeting sequences with GC content lower than the resident genome. Mutations in hns are lethal in Salmonella unless accompanied by compensatory mutations in other regulatory loci. Thus, H-NS provides a ...[more]
Similar Datasets
Project description:In the two F8 advanced crosses of broiler by Leghorn and broiler by Fayoumi, birds at day 1 were challenged with Salmonella enteritidis (SE). Spleen were collected at day 7 and 8. SE bacterial load in spleen were measured. Based on the bacterial load, birds were divided into high and low SE load groups. At each line cross and each day time point, three pair comparisons among high SE load, low SE load, and non-SE were used for the loop design, and two biological replicates were used.
2010-07-01 | E-GEOD-4273 | biostudies-arrayexpress
Project description:Our results demonstrate that RNase G controls expression levels of H-NS encoded by hns, strongly associated with the pathogenicity of S. Typhimurium. The hns mRNA abundance is mediated by RNase G, which cleaves the 5’-UTR of hns mRNA. In the upstream pathway, the induced expression of RNase G in host environment condition is attributable to reduced RNase III cleavage activity on rng mRNA. Our findings suggest the link between Salmonella pathogenicity and RNase III-RNase G pathway, underlining the importance of posttranscriptional regulation of H-NS in the downstream pathway, which controls Salmonella pathogenicity island-1 type III secretion system for the survival and virulence of S. Typhimurium in host cell.
2021-01-08 | PXD011090 | Pride
Project description:We have previously detected cyclin D1-initiated and p53-related (PERP; p53 apoptosis-associated target) cell death in a striatal 6-hydroxydopamine (6-OHDA)-treated Parkinsonian mouse model by adaptor-tagged competitive PCR (ATAC-PCR) (Synapse 51, 279-286, 2004). In order to establish the mechanism of dopaminergic cell death in Parkinsonâs disease, various Parkinsonian animal models should be studied. Therefore, the time-course alteration of gene expression in the substantia nigra pars compacta was investigated after a single administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) in common marmosets. In the MPTP model, gene expression of neither cyclin D1 nor PERP was altered. There were also few common alterations in gene expression between the MPTP and 6-OHDA models. This suggests that the mechanism of cell death may differ between these models, and extensive study in various Parkinsonian models should be performed to elucidate the mechanisms of dopaminergic cell death in Parkinsonâs disease. Experiment Overall Design: Materials and methods Experiment Overall Design: 1. Animals Experiment Overall Design: Five 3-year-old male common marmosets (Callithrix jacchus) weighing 350â400 g were used. A single marmoset was used as a vehicle-treated control, with the rest being administered MPTP. A microarray experiment and an immunohistochemical study were performed in the same animals. They were colonized in the Center for Life Science Resources in Kagoshima University, Japan. Animals were housed with free access to standard food in an air-conditioned room under a constant 12 h light/dark cycle (lights on at 7:00 a.m.) at a temperature of 25â27°C and 45â55% humidity. All efforts were made to minimize animal suffering, and to reduce the number of animals used. The present experiments were carried out after obtaining permission from the Committee of Animal Experimentation, Kagoshima University Graduate School of Medical and Dental Sciences, Japan. Experiment Overall Design: 2. MPTP administration Experiment Overall Design: A single dose of MPTP was administered intravenously (i.v.) to the animals in order to examine the time-course alteration in gene expression. As in our previous study, the dose of MPTP was 2.5 mg/kg (Nomoto et al., 1997). At this dose, animals exhibit immobility during an entire day, while doses greater than 2.5 mg/kg can induce death. MPTP hydrochloride (Sigma, St. Louis, MO, USA) was dissolved in 0.9% saline, and administered under intraperitoneal pentobarbital anesthesia (40 mg/kg). Under deep anesthesia with pentobarbital, the animals were decapitated either at 2 h, 6 h, 1 day or 14 days after MPTP administration. All experiments using MPTP were performed in accordance with safety guidelines (Przedborski et al., 2001). Experiment Overall Design: 3. Laser capture microdissection Experiment Overall Design: The midbrain of each marmoset was dissected on an ice-cold glass plate, and mounted on a specimen block with O.C.T. compound (Tissue-Tek, Sakura Finetechnical, Tokyo, Japan). The midbrains were frozen by covering them with very finely powdered dry ice. Sections (8 μm thickness) were cut on a cryostat (Microm HM500S, Carl Zeiss Japan, Tokyo, Japan), and mounted on ice-cold, membrane-coated glass slides (Carl Zeiss Japan). The membranes on the glass slides were coated with poly-L-lysine (P8920; Sigma). Immediately after mounting, slides were cooled on dry ice and stored at â80°C for less than 3 days. Slides were fixed in ethanol/acetate solution (19:1) at 4°C for 3 min, and washed with PBS at 4°C for 1 min. Slides were stained with 0.1% toluidine blue at room temperature for 10 s, washed with PBS at 4°C for 10 s, and then air-dried for 5 min. Immediately after staining, slides were processed for laser capture microdissection (LCM). Experiment Overall Design: A Leica AS LMD (Leica Microsystems, Wetzlar, Germany) was used for LCM. SNc sections corresponded to level A4.5 of the brain atlas (Stephan et al., 1980). These sections contained transverse sections of the oculomotor nerve. A strip of the unilateral SNc was dissected (Fig. 1). The SNcs from two slides were collected and placed in a PCR tube containing 10 μl extraction buffer of the PicoPure RNA Isolation Kit (Arcturus Bioscience, Mountain View, CA, USA). Experiment Overall Design: 4. Microarray experiments Experiment Overall Design: Total RNA was extracted by the PicoPure RNA Isolation Kit, and eluted in approximately 10 μl buffer, according to the manufacturerâs protocol. In order to obtain a sufficient amount of amplified RNA (aRNA) for the microarray experiments, total RNA was amplified using two rounds of in vitro transcription. The first round of amplification was performed using the RiboAmp HS RNA Amplification Kit (Arcturus). The second round of amplification used the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA, USA) and cyanine-3 or cyanine-5 labeling. The labeled aRNA was hybridized with Agilent whole human genome oligo microarray G4112A. In order to correct the buffer composition in the second round of amplification using the Low RNA Input Fluorescent Linear Amplification Kit, cDNA (11 μl) that was purified in the round 2 procedure by the RiboAmp HS RNA Amplification Kit, was added to the modified transcription buffer of the Agilent kit. Each sample contained 4 μl of 5 ï´ first strand buffer, 20 μl of 4 ï´ transcription buffer, 6 μl 0.1 M DTT, 8 μl NTP mix, 6.4 μl 50% PEG, 0.5 μl RNase inhibitor (RNase Out; Invitrogen, Carlsbad, CA, USA), 0.6 µl inorganic pyrophosphatase, 0.8 μl T7 RNA polymerase, 2.4 μl cyanine (PerkinElmer Life Sciences, Boston, MA, USA; cyanine-3 for controls and cyanine-5 for MPTP-treated marmosets), and 20.3 μl DW. Labeled aRNA was synthesized according to the instructions for the Agilent kit. Experiment Overall Design: An Agilent 2100 bioanalyzer and an RNA 6000 Pico LabChip Kit were used to examine the length distribution of labeled aRNAs. A preliminary experiment using the protocol found in the appendices of the HistoGene LCM Immunofluorescence Staining Kit (Arcturus) was performed to determine the degree of degradation of total RNA that occurred during tissue staining.
2008-06-13 | E-GEOD-5176 | biostudies-arrayexpress
Project description:We have compared the changes in cell cycle and cell death parameters induced by 2 different concentrations of 5-FU (IC50 and IC80) in the breast adenocarcinoma cell line MCF7. G1/S cell cycle arrest was associated with both concentrations, whereas cell death was mainly induced after IC80 5-FU. These changes were correlated with gene expression assessed by cDNA microarray analysis. Main findings included an overexpression of p53 target genes involved in cell cycle and apoptosis (CDKN1A/p21, TP53INP, TNFRSF6/FAS and BBC3/PUMA), and significant repression of Myc. High dose 5-FU also induced a higher regulation of the mitochondrial death genes APAF1, BAK1 and BCL2, and induction of genes of the ID family. Time and dose-dependent changes in gene expression, induced by 5-Fluorouracil, in breast carcinoma cell lines MCF7, and MDA-MB-435.
2010-07-01 | E-GEOD-2584 | biostudies-arrayexpress
Project description:The purpose of this experiment was to examine the differential transcriptional profiles of Caulobacter CB15N grown in M2-Glucose versus M2-Inositol. mRNA expression was compared between Caulobacter CB15N cells grown in M2-Glucose vs. M2-Inositol. Four arrays were run, two of each dye combination.
2010-06-30 | E-GEOD-12414 | biostudies-arrayexpress
Project description:Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem-cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila Kc cells. We found that Pc associates with large genomic regions of up to ~150kb in size, hereafter referred to as âPc-domainsâ. Sce and esc accompany Pc in most of these domains. PcG-bound chromatin is trimethylated at histone H3 lysine 27 and in general transcriptionally silent. Furthermore, PcG proteins preferentially bind to developmental genes. Many of these encode transcriptional regulators and key components of signal transduction pathways, including Wingless, Hedgehog, Notch and Delta. We also identify several new putative functions of PcG proteins, such as in steroid hormone biosynthesis. These results highlight the extensive involvement of PcG proteins in the coordination of development through the formation of large repressive chromatin domains. Keywords: DamID, Chromatin immunoprecipitation, ChIP-chip To study PcG binding profiles we used DamID, which is based on the ability of a chromatin protein fused to E.coli DNA adenine methyltransferase (Dam) to methylate the native binding site of the chromatin protein. Dam-fusion proteins are expressed at very low levels to avoid mistargeting. Subsequently, methylated DNA fragments are isolated, labeled and hybridized to a microarray. Methylated DNA fragments from cells transfected with Dam alone served as reference. Genomic binding sites of the protein can then be identified based on the targeted methylation pattern. For detailed background information on DamID, see: van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-8 (2001); van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8 (2000).
2010-06-11 | E-GEOD-4564 | biostudies-arrayexpress
Project description:The NimbleGen array contains 387,000 46~50-mer oligos, including 377,230 salmonella probes whose sequences only hit genome once. The probes were designed based on Salmonella typhimurium LT2 (NC_003197) genome, with a moving window of about 12 bases. Raw intensities were normalized by the median intensity in each channel and the ratios were calculated by log base 2 (hns-bound DNA / genomic DNA) after the normalization. Keywords: ChIP-chip
2006-05-23 | GSE4879 | GEO
Project description:Male embryos are reported to develop faster than female in the preimplantation stage. Therefore, male and female embryos can be considered phenotypically different as early as the preimplantation stage. Employing our sexing system of enhanced green fluorescent protein (EGFP) tagging X chromosomes, we compared the global gene expression pattern of male and female embryos at the blastocyst stage using DNA microarray. Experiment Overall Design: samples were collected from three independent preparations and the experiments were triplicated. Scanned microarray results were processed with Feature Extraction software (ver. 7.5, Agilent). ãThe hybridization experiments were duplicated in a reciprocal labeling manner to reduce dye integration bias, and total of six hybridizations were carried out for the entire analysis.ã Combining plural array results and statistical analyses were carried out by Luminator software (Rosetta).
2009-05-13 | E-GEOD-2934 | biostudies-arrayexpress
Project description:Duplication of genes encoding transcription factors plays an essential role in driving phenotypic variation. Because regulation can occur at multiple levels, it is often difficult to discern how each duplicated factor achieves its regulatory specificity. In these cases, a systems approach may distinguish the role of each factor by integrating complementary large-scale measurements of the regulatory network. To explore such an approach, we integrate growth phenotypes, promoter binding profiles, and gene expression patterns to model the DNA damage response network controlled by the Yeast-specific AP-1 (YAP) family of transcription factors. This analysis reveals that YAP regulatory specificity is achieved by at least three mechanisms: (a) Divergence of DNA-binding sequences into two subfamilies; (b) Condition-specific combinatorial regulation by multiple Yap factors; and (c) Interactions of Yap 1, 4, and 6 with chromatin remodeling proteins. Additional microarray experiments establish that Yap4 and 6 regulate gene expression through interactions with the histone deacetylase, Hda1. The data further highlight differences among Yap paralogs in terms of their regulatory mode of action (activation vs. repression). This study suggests how other large TF families might be disentangled in the future. Keywords: gene expression microarray and ChIP-chip Gene expression of wild type and single YAP deletion (YAP1/2/4/5/6) strains were profiled in media supplemented with either MMS or CDDP at two different concentrations. ChIP-chip of five YAPs (YAP1/2/4/6/6) were done in duplicate in both drug-treated (MMS or CDDP) or untreated (SC media) conditions.
2008-02-03 | E-GEOD-10146 | biostudies-arrayexpress
Project description:Gene content in Salmonella enterica sv Typhimurium 14028s after treatment with 2mM hydrogen peroxide
2010-06-09 | E-GEOD-811 | biostudies-arrayexpress