Journal ArticleDOI
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
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TLDR
DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions.Abstract:
DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration. The expression profiles observed for genes with known metabolic functions pointed to features of the metabolic reprogramming that occur during the diauxic shift, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions. The same DNA microarrays were also used to identify genes whose expression was affected by deletion of the transcriptional co-repressor TUP1 or overexpression of the transcriptional activator YAP1. These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns.read more
Citations
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Donuts, scratches and blanks: robust model-based segmentation of microarray images
TL;DR: A new robust model-based method for processing microarray images so as to estimate foreground and background intensities and provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three.
Journal ArticleDOI
Sip4, a Snf1 kinase‐dependent transcriptional activator, binds to the carbon source‐responsive element of gluconeogenic genes
Olivier Vincent,Marian Carlson +1 more
TL;DR: The carbon source‐responsive element (CSRE) mediates transcriptional activation of the gluconeogenic genes during growth of the yeast Saccharomyces cerevisiae on non‐fermentable carbon sources and Sip4, a glucose‐regulated C6 zinc cluster activator, is identified by its interaction with the Snf1 protein kinase.
Journal ArticleDOI
Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl.
Melissa H. Jia,Robert A. LaRossa,Jian-Ming Lee,Antoni Rafalski,Ellen J. Derose,Greg Gonye,Zhixiong Xue +6 more
TL;DR: A potential link between SM sensitivity and ergosterol metabolism was uncovered by expression profiling and confirmed by genetic analysis, suggesting a serious cellular consequence.
Journal ArticleDOI
Cloning and functional expression of UGT genes encoding sterol glucosyltransferases from Saccharomyces cerevisiae, Candida albicans, Pichia pastoris, and Dictyostelium discoideum.
Dirk Warnecke,Ralf Erdmann,Annette Fahl,Bernhard Hube,Frank Müller,Thorsten K. Zank,Ulrich Zähringer,Ernst Heinz +7 more
TL;DR: In vitro enzyme assays with cell-free extracts of the transgenic E. coli strains showed that the genes encode UDP-glucose:sterol glucosyltransferases which can use different sterols such as cholesterol, sitosterol, and ergosterol as sugar acceptors and prove that sterol glucOSide synthesis is an inherent feature of eukaryotic microorganisms.
Journal ArticleDOI
A Novel CRP-dependent Regulon Controls Expression of Competence Genes in Haemophilus influenzae
Rosemary J. Redfield,Andrew D. S. Cameron,Qing Qian,J. Hinds,Tahir Ali,J. Simon Kroll,Paul R. Langford +6 more
TL;DR: Competence-induced transcription of genes in the CRE regulon is strongly dependent on cAMP, consistent with the known role of catabolite regulation in competence, and electrophoretic mobility-shift assays confirmed that CRE sequences are a new class of CRP-binding site.
References
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Journal ArticleDOI
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TL;DR: A high-capacity system was developed to monitor the expression of many genes in parallel by means of simultaneous, two-color fluorescence hybridization, which enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA.
PatentDOI
Expression monitoring by hybridization to high density oligonucleotide arrays
TL;DR: In this article, the authors proposed a method for monitoring the expression levels of a multiplicity of genes by hybridizing a nucleic acid sample to a high density array of oligonucleotide probes and quantifying the hybridized nucleic acids in the array.
Journal ArticleDOI
Use of a cDNA microarray to analyse gene expression patterns in human cancer.
Joseph L. DeRisi,Lolita Penland,Patrick O. Brown,M. L. Bittner,P. S. Meltzer,M. Ray,Yi Chen,Y. A. Su,J. M. Trent +8 more
TL;DR: Previously unrecognized alterations in the expression of specific genes provide leads for further investigation of the genetic basis of the tumorigenic phenotype of these cells.
Journal ArticleDOI
Accessing Genetic Information with High-Density DNA Arrays
Mark S. Chee,Robert Yang,Earl Hubbell,Anthony Berno,Xiaohua C. Huang,David Stern,Jim Winkler,David J. Lockhart,Macdonald S. Morris,Stephen P. A. Fodor +9 more
TL;DR: The simultaneous analysis of the entire human mitochondrial genome is described here and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability.
Journal ArticleDOI
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.
TL;DR: This work describes a general experimental approach, using microscopic arrays of DNA fragments on glass substrates for differential hybridization analysis of fluorescently labeled DNA samples, and demonstrates the utility of DNA microarrays in the analysis of complex DNA samples.