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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Journal ArticleDOI
Identification of mitochondrial carriers in Saccharomyces cerevisiae by transport assay of reconstituted recombinant proteins
Ferdinando Palmieri,Gennaro Agrimi,Emanuela Blanco,Alessandra Castegna,Maria Antonietta Di Noia,Vito Iacobazzi,Francesco M. Lasorsa,Carlo M.T. Marobbio,Luigi Palmieri,Pasquale Scarcia,Simona Todisco,Angelo Vozza,John E. Walker +12 more
TL;DR: This review describes how the functions of 15 of these previously unknown transport proteins have been determined by a strategy that consists of expressing the genes in Escherichia coli or Saccharomyces cerevisiae, reconstituting the gene products into liposomes and establishing their functions by transport assay.
Journal ArticleDOI
Estimating genomic coexpression networks using first-order conditional independence
TL;DR: A complementary unsupervised graph search algorithm for discovering locally distinct sub graphs of a large weighted graph is described and it is shown that subgraphs found using this approach correspond to particular biological processes or contain representatives of distinct gene families.
Journal ArticleDOI
Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli.
Taku Oshima,Chieko Wada,Yuya Kawagoe,Takeshi Ara,Maki Maeda,Yasushi Masuda,Sota Hiraga,Hirotada Mori +7 more
TL;DR: It is proposed that Dam‐mediated methylation plays an important role in the global regulation of genes, particularly those with Fnr and CRP binding sites, particularly the ones associated with fumarate nitrate reduction and catabolite activator protein (CRP).
Journal ArticleDOI
A second iron-regulatory system in yeast independent of Aft1p
TL;DR: Yeast has a second regulatory pathway for the iron regulon, with AFT1 and AFT2 playing partially redundant roles, according to kinetics of induction of two genes activated by the A FT2-1up allele, which are consistent with Aft2p acting as a direct transcriptional factor.
Journal ArticleDOI
Std1 and Mth1 proteins interact with the glucose sensors to control glucose-regulated gene expression in Saccharomyces cerevisiae
Martin C. Schmidt,Rhonda R. McCartney,Xudong Zhang,Tommy S. Tillman,Harry Solimeo,Stefan Wölfl,Ciprian Almonte,Simon C. Watkins +7 more
TL;DR: Genetic interactions between STD1, MTH1, SNF3, andRGT2 suggest that the glucose signaling is mediated, at least in part, through interactions of the products of these four genes.
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.