Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR588534_1.fastq.gz | Fastqsanger.gz | |||
| ERR588534_2.fastq.gz | Fastqsanger.gz | |||
| ERR588535_1.fastq.gz | Fastqsanger.gz | |||
| ERR588535_2.fastq.gz | Fastqsanger.gz | |||
| ERR598471_1.fastq.gz | Fastqsanger.gz |
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Project description:The threat of viral pandemics demands a comprehensive understanding of evolution at the host-pathogen interface. Here, we systematically show that the accessibility of adaptive mutations in influenza nucleoprotein at fever-like temperatures is mediated by host chaperones. Particularly noteworthy, we observe that the Pro283 nucleoprotein variant, which is conserved across human flu strains, confers resistance to the MxA antiviral-restriction factor, and critically contributed to the pathogenicity of the 1918 pandemic flu, is rendered unfit by host chaperone depletion. This fitness loss is linked to biophysical defects that chaperones cannot address when heat shock factor-I is inhibited. Thus, host chaperones can be hijacked by viruses to un-couple biophysically deleterious consequences of mutations from the benefits of immune escape. In summary, host chaperones play a central role in shaping influenza adaptation, with implications for the evolution of other viruses, for viral host-switching, and for the design of antiviral strategies refractory to resistance.
2018-09-10 | GSE113649 | GEO
Project description:Accumulation of deleterious mutations during bacterial range expansions
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Project description:In diploid organisms, selfing reduces the efficiency of selection in purging deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme from of selfing known as intragametophytic selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Using the transcriptome data from S. subsecundum, S. cribrosum and 2 other previously published moss transcriptome, we ask how effectively deleterious mutations are purged from such plants. Specifically, we study genome-wide signatures of selective purging in the transcriptomes of four moss species that differ in their incidence of selfing and outcrossing.
2014-06-30 | E-MTAB-2482 | biostudies-arrayexpress
Project description:Oncohistone mutations are crucial drivers for tumorigenesis, but how a living organism responds to and governs the loss-of-function oncohistone remains unclear. Here, we generated a histone H2B triple knockout (3KO) strain in Caenorhabditis elegans, which decreased the embryonic H2B level, disrupted cell divisions, and caused animal sterility. Our genetic screens identified mutations defective in a histone H3-H4 chaperone UNC-85 as suppressors that recovered H2B 3KO fertility. We found that unc-85 mutations reduced chromatin H3-H4 levels and that inhibiting other H3-H4 chaperones or H3-H4 histones also rescued H2B 3KO sterility. The oncohistone H2BE76K mutation disrupts the H2B-H4 interface and causes nucleosome instability, and we showed that blocking H3-H4 chaperones restored cell division defects in C. elegans or human cells carrying H2BE76K. Thus, our results indicate that reducing chromatin H3-H4 rescues H2B loss and suggest that inhibiting H3-H4 chaperones may be a therapeutic strategy to treat cancers resulting from loss-of-function H2B oncohistone.
2022-04-03 | GSE185582 | GEO
Project description:Protein aggregation is a complex phenomenon involving aberrant folding and proteostasis that leads to various proteopathies. Despite extensive efforts, the maintenance of protein solubility against aggregation remains ill-defined, especially in complex cellular environments. In this study, we show that the depletion of RNAs from Escherichia coli lysates results in global protein aggregation. Using quantitative mass spectroscopic analysis, we identified significant proteins (>900) from the whole E. coli proteome whose solubility maintenance is dependent on RNA. Proteome-wide characterization revealed that RNA dependence was highly enriched among acidic proteins, intrinsically disordered proteins, and structural hub proteins. Notably, the solubility of representative molecular chaperones [Trigger factor (TF), DnaJ, and GroES] is largely dependent on RNA, suggesting a hitherto unknown hierarchical relationship between RNA-based chaperone (chaperna) and protein-based molecular chaperones. Our findings provide new insights into proteome solubility maintenance and misfolding-associated proteopathy in vivo, where proteins, from birth to death, stably or transiently associate with RNAs.
2024-05-24 | PXD040618 | Pride
Project description:The histone chaperones play an important role in chromatin assembly and disassembly during replication and transcription. We assessed the global roles of histone chaperones in Saccharomyces cerevisiae. Microarray transcriptional analyses indicate that histone chaperones have their own specific target genes, and various histone chaperones have partially overlapping functions during transcriptional regulation. Histone deacetylase inhibitor TSA and histone chaperones Asf1, Vps75 and Rtt106 can function in parallel pathways to regulate transcription. Moreover, TSA can specifically antagonize histone chaperone Chz1-mediated telomere anti-silencing. This study demonstrates that a mutual cross-talk mechanism exists between histone chaperones and histone deacetylation in transcriptional regulation. All yeast strains used in this study are listed in the paper (Table S1). CHZ1, NAP1, ASF1, VPS75 and RTT106 genes were deleted individually by homologous recombination in BY4742 (WT) by using a previously described in (Wan, Y. et al. MCB, 2009) PCR-based procedure. The strains were cultured at 30°C in YPD (1% yeast extract, 2% peptone, 2% glucose) media. For TSA treatments, WT and deletion mutants were grown to mid-log phase (OD600=0.5), TSA (Sigma-Aldrich) was then added to the yeast cultures at a final concentration of 10 ?M and cells were cultured for additional hour.Total RNA was isolated by hot acid phenol extraction protocol as previously described in Wan, Y. et al. MCB, 2009. Microarray labeling and hybridization reactions were performed as previously described in Wan, Y. et al. MCB, 2009 and Wan, Y. et al. NAR, 2010. Two color microarrays, comparing RNA from the experimental conditions (deletion mutations grown in YPD, WT and deletion mutations grown in YPD with TSA treatment) to RNA from the control WT cells grown in glucose-containing medium (YPD), were performed using Agilent whole-genome S. cerevisiae arrays.
2011-06-28 | E-GEOD-30228 | biostudies-arrayexpress
Project description:Structure probing experiments were performed on in vitro transcripts and E. coli and human cell cultures under natively extracted (cell-free) and in-cell conditions to benchmark the performance of the newly introduced PAIR-MaP correlated chemical probing strategy for detecting RNA duplexes. Multiple-hit dimethyl sulfate (DMS) probing was done using new buffer conditions that facilitate DMS modification of all four nucleotides.
2019-08-01 | GSE135211 | GEO
Project description:Goal of experiment: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference). Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice. Preparation of cDNA. Double-stranded cDNA was synthesized from purified RNA. The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes. Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl. Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen). A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated. Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA. The following mix was incubated at 37°C for 5 hours: 1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase. Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts. Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C. (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc). After fragmentation, the samples were stored at -20°C until the hybridization was performed. Sample hybridization. Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice. For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen), 0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl). Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation. After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm. Washing and staining of array. The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C. Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20). (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker). Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20). Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]). Analysis. After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix). Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis. Keywords = BWF1 total spleen Keywords: repeat sample
2005-08-23 | GSE2336 | GEO
Project description:Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy.
2015-06-18 | GSE69912 | GEO
Project description:Isolated perfused and ventilated BALB/c mouse lung model 3 conditions c-10cmH2O pressure ventilation 3h, LPS-10cmH2O pressure ventilation 3h in the presence of E. coli LPS in the perfusion buffer (3mg/kg), ov-overventilation with 25cmH2O pressure 3h Keywords: parallel sample
2005-05-10 | GSE2635 | GEO