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ABSTRACT:
PROVIDER: PRJNA283424 | ENA |
REPOSITORIES: ENA
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Project description:Genome-wide reprogramming of transcript architecture by temperature specifies the developmental states of the human pathogen Histoplasma [ribosome profiling]
| PRJNA283425 | ENA
Project description:Genome-wide reprogramming of transcript architecture by temperature specifies the developmental states of the human pathogen Histoplasma [transcriptional profiling]
| PRJNA283426 | ENA
Project description:Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel post-transcriptional mechanism of gene regulation in Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5’ leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements uncovered a class of differential leader transcripts that exhibit tight transcriptional and translational regulation. Further examination of these dually regulated genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature. This series contains ribosomal footprinting data for Hc G217B.
2015-07-16 | GSE68705 | GEO
Project description:Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel post-transcriptional mechanism of gene regulation in Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5’ leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements uncovered a class of differential leader transcripts that exhibit tight transcriptional and translational regulation. Further examination of these dually regulated genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature. This series contains expression profiling data for four strains of Hc.
2015-07-16 | GSE68706 | GEO
Project description:Nitrate is the limiting nitrogen nutrient enabling photosynthetic plants to support the conversion of inorganic elements to organic biomass, which sustains all lives. Plants evolved multifaceted nitrate responses to modulate global gene expression, metabolism and developmental programs. However, primary nitrate signaling mechanisms remained elusive. Using an ultrasensitive Ca2+ biosensor, unique nitrate-induced Ca2+ signaling was illuminated in Arabidopsis cells and plants. Integrative functional genomic screens, chemical genetics, genome-wide transcript sequencing, and analyses of nitrate-associated traits uncovered the surprising roles of Ca2+ sensor protein kinases (CPKs) in orchestrating diverse primary and long-term nitrate responses. Nitrate specifies CPK signaling to reprogram transcriptome and govern N-assimilation, metabolism, transport, hormones, shoot growth, and root system architecture. CPKs may be targeted to enhance nitrogen-use-efficiency, reduce fertilizer demands, and alleviate ecosystem pollution.
2017-05-19 | GSE73437 | GEO
Project description:The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genome-wide studies to experimentally validate its genome annotation. A functional interrogation of the Histoplasma genome provides critical support for continued investigation into the biology and pathogenesis of H. capsulatum and related fungi. We employed a three-pronged approach to provide a functional annotation for the H. capsulatum G217B strain. First, we probed high-density tiling arrays with labeled cDNAs from cells grown under diverse conditions. These data defined 6,172 transcriptionally active regions (TARs), providing validation of 6,008 gene predictions. Interestingly, 22% of these predictions showed evidence of anti-sense transcription. Additionally, we detected transcription of 264 novel genes not present in the original gene predictions. To further enrich our analysis, we incorporated expression data from whole-genome oligonucleotide microarrays. These expression data included profiling under growth conditions that were not represented in the tiling experiment, and validated an additional 2,249 gene predictions. Finally, we compared the G217B gene predictions to other available fungal genomes, and observed that an additional 254 gene predictions had an ortholog in a different fungal species, suggesting that they represent genuine coding sequences. These analyses yielded a high confidence set of validated gene predictions for H. capsulatum. The transcript sets resulting from this study are a valuable resource for further experimental characterization of this ubiquitous fungal pathogen. The data is available for interactive exploration at http://histo.ucsf.edu. The non-redundant genome sequence of Histoplasma capsulatum G217B was tiled over a set of 93 CombiMatrix arrays, which were then hybridized with labeled cDNA samples from yeast-form (red channel) or mycelial-form (green channel) Histoplasma. Due to low yields from the mycelial samples, only the red channel intensities were analyzed (and the red foreground intensities are, therefore, reported in the VALUE column for each sample). Rather than normalizing intensities across arrays, each probe was evaluated as detected or undetected relative to the negative control intensities on the corresponding array, and the density of detected probes as a function of genome position was used for the remaining analysis.
2011-08-11 | E-GEOD-31155 | biostudies-arrayexpress
Project description:Using RNA-seq we report the global changes that occur in response to host temperature stress in the pathogen, Crypococcus neoformans, and reveal that mRNA decay plays a critical role in the transcriptomic and translatomic reprogramming necessary for stress adaptation.
2019-09-26 | GSE121183 | GEO
Project description:The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genome-wide studies to experimentally validate its genome annotation. A functional interrogation of the Histoplasma genome provides critical support for continued investigation into the biology and pathogenesis of H. capsulatum and related fungi. We employed a three-pronged approach to provide a functional annotation for the H. capsulatum G217B strain. First, we probed high-density tiling arrays with labeled cDNAs from cells grown under diverse conditions. These data defined 6,172 transcriptionally active regions (TARs), providing validation of 6,008 gene predictions. Interestingly, 22% of these predictions showed evidence of anti-sense transcription. Additionally, we detected transcription of 264 novel genes not present in the original gene predictions. To further enrich our analysis, we incorporated expression data from whole-genome oligonucleotide microarrays. These expression data included profiling under growth conditions that were not represented in the tiling experiment, and validated an additional 2,249 gene predictions. Finally, we compared the G217B gene predictions to other available fungal genomes, and observed that an additional 254 gene predictions had an ortholog in a different fungal species, suggesting that they represent genuine coding sequences. These analyses yielded a high confidence set of validated gene predictions for H. capsulatum. The transcript sets resulting from this study are a valuable resource for further experimental characterization of this ubiquitous fungal pathogen. The data is available for interactive exploration at http://histo.ucsf.edu.
2011-08-12 | GSE31155 | GEO
Project description:High temperature influences plant development and can reduce crop yields. We used the Agilent Barley Gene Expression Microarray to identify high temperature responsive genes in cereals. In temperate cereals, such as wheat and barley, high temperature results in rapid progression through reproductive development in long-days but inhibits early stages of reproductive development in short-days. We examined the transcriptome of barley plants grown at two different temperatures, 15°C or 25°C, in either long or short-days. Under these conditions early reproductive development was accelerated by high temperature in long-days but inhibited by high temperature in short-days. To control for the effect of temperature on vegetative growth, plants were sampled at the same stage of vegetative development (leaf emergence) in all treatments. Transcriptome analysis identified genes that show changed transcript levels in response to daylength (long versus short-days), genes that show changed transcript levels in response to temperature (15°C versus 25°C), and small groups of genes that show changed transcript levels only in response to specific combinations of daylength and temperature. For example, genes that are upregulated only under long-days and high temperature: conditions in which early reproductive development proceeds rapidly. The temperature responsive genes identified here offer potential candidates for developmental regulators controlling the developmental response of cereal crops to high temperatures.
2012-04-04 | GSE33938 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE34091: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [Mouse430_2 Expression] GSE34092: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [MoGene-1_0 Expression] GSE34094: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq] Refer to individual Series
2012-07-24 | E-GEOD-34093 | biostudies-arrayexpress