Genome-wide Screen (genome-wide + screen)

Distribution by Scientific Domains


Selected Abstracts


Genome-wide screen identifies Escherichia coli TCA-cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA

AGING CELL, Issue 5 2010
Stavros Gonidakis
Summary Single-gene mutants with extended lifespan have been described in several model organisms. We performed a genome-wide screen for long-lived mutants in Escherichia coli, which revealed strains lacking tricarboxylic acid (TCA)-cycle-related genes that exhibit longer stationary-phase survival and increased resistance to heat stress compared to wild-type. Extended lifespan in the sdhA mutant, lacking subunit A of succinate dehydrogenase, is associated with the reduced production of superoxide and increased stress resistance. On the other hand, the longer lifespan of the lipoic acid synthase mutant (lipA) is associated with reduced oxygen consumption and requires the acetate-producing enzyme pyruvate oxidase, as well as acetyl-CoA synthetase, the enzyme that converts extracellular acetate to acetyl-CoA. The hypoxia-inducible transcription factor ArcA, acting independently of acetate metabolism, is also required for maximum lifespan extension in the lipA and lpdA mutants, indicating that these mutations promote entry into a mode normally associated with a low-oxygen environment. Because analogous changes from respiration to fermentation have been observed in long-lived Saccharomyces cerevisiae and Caenorhabditis elegans strains, such metabolic alterations may represent an evolutionarily conserved strategy to extend lifespan. [source]


4413: Analysis of gene expression in acute ischemic neuroretinas : a genome-wide screen discriminating occlusion (BRVO) versus laser effects in rats

ACTA OPHTHALMOLOGICA, Issue 2010
C OROPESA
Purpose Identification of genes differentially regulated in rat neuroretinas submitted to an experimental acute branch retinal vein occlusion (BRVO), to a laser treatment, or to no treatment at all. Methods We have developed an in vivo experimental model of venous occlusion by photodynamic thrombosis in rat retinas. After anaesthesia, a sodium fluorescein solution was injected in rat tail 15 minutes before laser treatments. To induce ischemia in tested retina, venous sites adjacent to the optic nerve head were photocoagulated with an argon laser. In one group of tested animals, the retina was exposed to laser treatment at sites located between major vessels. As this treatment may have an effect upon choroidal blood flow, control eyes were not subjected to laser treatment. RNAs were isolated from the neuroretina 30 minutes post treatments, and processed for Affymetrix gene-chip analysis. Results Genome-wide screen enabled us to identify 308 and 348 genes which were up- or down-regulated, respectively, by BRVO and laser treatment only. When we compared the transcriptomes of retinas subjected to vessel occlusion or laser treatment to the control one, we found that the expression profiles of, respectively, 116 and 126 genes were specifically modified. The majority of the up- and down-regulated genes encode proteins involved in different aspects of early stress response, neuroprotection, inflammation and apoptosis. Conclusion Our microarray analysis revealed changes in gene expression bearing similarities to gene expression results from other ischemia models. Furthermore, it revealed that laser treatment may have an unreported impact on retina's metabolism. [source]


Regulation of retinal ganglion cell gene expression by bHLH transcription factors in the developing and ischemic retinas

ACTA OPHTHALMOLOGICA, Issue 2009
JM MATTER
Purpose The loss of retinal ganglion cells (RGC) in the glaucomatous retina exhibits similarities to the pattern of neuronal degeneration detected after experimental ischemia. However, a short episode of retinal ischemia does not provoke damage but rather triggers an endogenous form of neuroprotection. HIFs are bHLH proteins that regulate hypoxic response in ischemic retinas and they are involved in neuroprotection. Hypoxic environments also occur in the developing embryo and create specific niches controlling cell differentiation. Genetic analyses of HIF functions have revealed the importance of oxygen as a key regulator of ontogeny. We have compared the transcriptomes of RGCs in ischemic versus developing retinas. Methods Genome-wide screens were conducted to identify genes which are expressed in newborn RGCs and growing optic nerve axons and which are up- or down-regulated after venal occlusion by photodynamic thrombosis in the rat retinas. Results Atoh7 is a bHLH protein which is central to the transcriptional network regulating the production of RGCs. Among the targets of Atoh7 there are genes involved in the general metabolism and energy supply , e.g., alpha-enolase (ENO1), glucose-6 -phosphate isomerase (GPI). These glycolytic enzymes are also targets of HIFs and they are upregulated during hypoxia. To investigate the linkage of glycolysis and mitochondrial activity in RGCs, we monitored by confocal time-lapse imaging the dynamic distribution of mitochondria in the cell bodies and axons of RGCs that express HIF/Atoh7 targets in developing and ischemic retinas. Conclusion Some gene expression programs involved in differentiating RGCs might be reinitiated in neuroprotection. [source]


Mutations in TREM2 lead to pure early-onset dementia without bone cysts,

HUMAN MUTATION, Issue 9 2008
Eliane Chouery
Abstract A genome-wide screen using 382 STR markers to localize and identify the gene implicated in early-onset dementia (EOD) without bone cysts in a Lebanese family with three affected subjects was conducted. A unique locus homozygous by descent at chromosome 6p21.2 locus was identified. Candidate genes were explored by fluorescent sequencing and the effect of the identified mutation was confirmed by qualitative and quantitative RT-PCR. The genetic analysis revealed a novel deletion, c.40+3delAGG, in the 5' consensus donor splice site in intron 1 of TREM2 gene which is known to be responsible for PLOSL (Polycystic Lipomembranous Osteodysplasia with Sclerosing Leukoencephalopathy) also designated as Nasu-Hakola disease. In silico analysis predicted a lower strength for the novel donor splice site. Qualitative RT-PCR revealed normal transcript while quantitative RT-PCR showed over twofold down-regulation of TREM2 transcripts. The expression profile of six genes SPP1, NEDD9, FSCN, BCL3, NFKBIA and CCL2 known as disrupted in TREM2-deficient samples was studied and showed same expression profile as TREM2-mutated samples except for CCL2 which was normally regulated. The significantly-reduced expression of TREM2 in our patients and the expression profiles of the six studied genes confirm a role for TREM2 in this distinct phenotype of EOD without bone cysts. To our knowledge, this is the first report of mutations in TREM2 causing a pure dementia. © 2008 Wiley-Liss, Inc. [source]


Genome-wide screen identifies Escherichia coli TCA-cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA

AGING CELL, Issue 5 2010
Stavros Gonidakis
Summary Single-gene mutants with extended lifespan have been described in several model organisms. We performed a genome-wide screen for long-lived mutants in Escherichia coli, which revealed strains lacking tricarboxylic acid (TCA)-cycle-related genes that exhibit longer stationary-phase survival and increased resistance to heat stress compared to wild-type. Extended lifespan in the sdhA mutant, lacking subunit A of succinate dehydrogenase, is associated with the reduced production of superoxide and increased stress resistance. On the other hand, the longer lifespan of the lipoic acid synthase mutant (lipA) is associated with reduced oxygen consumption and requires the acetate-producing enzyme pyruvate oxidase, as well as acetyl-CoA synthetase, the enzyme that converts extracellular acetate to acetyl-CoA. The hypoxia-inducible transcription factor ArcA, acting independently of acetate metabolism, is also required for maximum lifespan extension in the lipA and lpdA mutants, indicating that these mutations promote entry into a mode normally associated with a low-oxygen environment. Because analogous changes from respiration to fermentation have been observed in long-lived Saccharomyces cerevisiae and Caenorhabditis elegans strains, such metabolic alterations may represent an evolutionarily conserved strategy to extend lifespan. [source]


Priming of plant innate immunity by rhizobacteria and ,-aminobutyric acid: differences and similarities in regulation

NEW PHYTOLOGIST, Issue 2 2009
Sjoerd Van der Ent
Summary ,,Pseudomonas fluorescens WCS417r bacteria and ,-aminobutyric acid can induce disease resistance in Arabidopsis, which is based on priming of defence. ,,In this study, we examined the differences and similarities of WCS417r- and ,-aminobutyric acid-induced priming. ,,Both WCS417r and ,-aminobutyric acid prime for enhanced deposition of callose-rich papillae after infection by the oomycete Hyaloperonospora arabidopsis. This priming is regulated by convergent pathways, which depend on phosphoinositide- and ABA-dependent signalling components. Conversely, induced resistance by WCS417r and ,-aminobutyric acid against the bacterial pathogen Pseudomonas syringae are controlled by distinct NPR1-dependent signalling pathways. As WCS417r and ,-aminobutyric acid prime jasmonate- and salicylate-inducible genes, respectively, we subsequently investigated the role of transcription factors. A quantitative PCR-based genome-wide screen for putative WCS417r- and ,-aminobutyric acid-responsive transcription factor genes revealed distinct sets of priming-responsive genes. Transcriptional analysis of a selection of these genes showed that they can serve as specific markers for priming. Promoter analysis of WRKY genes identified a putative cis -element that is strongly over-represented in promoters of 21 NPR1-dependent, ,-aminobutyric acid-inducible WRKY genes. ,,Our study shows that priming of defence is regulated by different pathways, depending on the inducing agent and the challenging pathogen. Furthermore, we demon-strated that priming is associated with the enhanced expression of transcription factors. [source]


Assignment of the locus for arachnomelia syndrome to bovine chromosome 23 in Simmental cattle

ANIMAL GENETICS, Issue 6 2009
J. Buitkamp
Summary Arachnomelia syndrome is a lethal inherited malformation mainly of the limbs, vertebral column and skull in cattle, which poses a severe impairment to farmers and breeders. Recently, a number of cases of arachnomelia syndrome have occurred in the Simmental breed and some sires with excellent breeding values had been shown to be carriers of the disease. We herein report the genetic mapping of the mutation underlying arachnomelia in cattle. The disease was mapped using a two-stage genome scan. A first round autosomal genome-wide screening using a limited number of cases identified three chromosomal regions with lod-scores > 1. The position of the arachnomelia syndrome locus was identified to be on BTA 23 by genotyping an additional, independent set of animals with markers that provided positive lod-scores in the course of the initial genome-wide screen. Using a denser set of regional microsatellites, the locus could be mapped to a region about 9 cM in length. The most significant linkage signal with arachnomelia syndrome was obtained with marker NRKM-17 (lod-score > 20) using a recessive model. Interestingly, different genes seem to be responsible for the disease in Brown Swiss and Simmental breeds, as arachnomelia syndrome was mapped to a different location in Brown Swiss. The results provide sufficient information for the development of a genetic test system and also allow the identification of positional candidate genes. [source]


Audioprofiling identifies TECTA and GJB2 -related deafness segregating in a single extended pedigree

CLINICAL GENETICS, Issue 2 2007
NC Meyer
An audioprofile displays phenotypic data from several audiograms on a single graph that share a common genotype. In this report, we describe the application of audioprofiling to a large family in which a genome-wide screen failed to identify a deafness locus. Analysis of audiograms by audioprofiling suggested that two persons with hearing impairment had a different deafness genotype. On this basis, we reassigned affectation status and identified a p.Cys1837Arg autosomal dominant mutation in ,-tectorin segregating in all family members except two persons, who segregated autosomal recessive deafness caused by p.Val37Ile and p.Leu90Pro mutations in Connexin 26. One nuclear family in the extended pedigree segregates both dominant and recessive non-syndromic hearing loss. [source]


Examination of tetrahydrobiopterin pathway genes in autism

GENES, BRAIN AND BEHAVIOR, Issue 8 2009
N. C. Schnetz-Boutaud
Autism is a complex disorder with a high degree of heritability and significant phenotypic and genotypic heterogeneity. Although candidate gene studies and genome-wide screens have failed to identify major causal loci associated with autism, numerous studies have proposed association with several variations in genes in the dopaminergic and serotonergic pathways. Because tetrahydrobiopterin (BH4) is the essential cofactor in the synthesis of these two neurotransmitters, we genotyped 25 SNPs in nine genes of the BH4 pathway in a total of 403 families. Significant nominal association was detected in the gene for 6-pyruvoyl-tetrahydropterin synthase, PTS (chromosome 11), with P = 0.009; this result was not restricted to an affected male-only subset. Multilocus interaction was detected in the BH4 pathway alone, but not across the serotonin, dopamine and BH4 pathways. [source]


The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae

JOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2010
D. Stanley
Summary Saccharomyces cerevisiae is traditionally used for alcoholic beverage and bioethanol production; however, its performance during fermentation is compromised by the impact of ethanol accumulation on cell vitality. This article reviews studies into the molecular basis of the ethanol stress response and ethanol tolerance of S. cerevisiae; such knowledge can facilitate the development of genetic engineering strategies for improving cell performance during ethanol stress. Previous studies have used a variety of strains and conditions, which is problematic, because the impact of ethanol stress on gene expression is influenced by the environment. There is however some commonality in Gene Ontology categories affected by ethanol assault that suggests that the ethanol stress response of S. cerevisiae is compromised by constraints on energy production, leading to increased expression of genes associated with glycolysis and mitochondrial function, and decreased gene expression in energy-demanding growth-related processes. Studies using genome-wide screens suggest that the maintenance of vacuole function is important for ethanol tolerance, possibly because of the roles of this organelle in protein turnover and maintaining ion homoeostasis. Accumulation of Asr1 and Rat8 in the nucleus specifically during ethanol stress suggests S. cerevisiae has a specific response to ethanol stress although this supposition remains controversial. [source]


Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

MOLECULAR MICROBIOLOGY, Issue 1 2009
Kai Papenfort
Summary The small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome-wide screens in Escherichia coli and Salmonella. Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial ,core' small RNA, yet its function remained unknown. Here, we report that ArcZ acts as a post-transcriptional regulator in Salmonella, repressing the mRNAs of the widely distributed sdaCB (serine uptake) and tpx (oxidative stress) genes, and of STM3216, a horizontally acquired methyl-accepting chemotaxis protein (MCP). Both sdaCB and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the tpx mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an arcZ deletion strain further argued for the existence of a distinct set of Salmonella loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady-state levels of > 16% (> 750) of all Salmonella mRNAs, and rendered the bacteria non-motile. Deep sequencing detected a dramatically changed profile of Hfq-bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post-transcriptional regulation. [source]