The application of DNA microarrays in gene expression analysis

Hal, Nicole L.W. Van; Vorst, Oscar; Houwelingen, A.M.M.L. van; Kok, E.J.; Peijnenburg, Ad; Aharoni, Asaph; Tunen, Arjen J. van; Keijer, Jaap

doi:10.1016/s0168-1656(00)00204-2

Cited by 199 publications

(95 citation statements)

References 39 publications

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“…DNA microarrays are becoming widely used tools in gene expression analysis (50). To study differential gene expression in BAT and WAT, microarrays were produced containing the 110 clones from DP2 and 146 clones from DP3.…”

Section: Generation Of a Cdna Library Of Candidate Genesmentioning

confidence: 99%

Differential gene expression in white and brown preadipocytes

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Klingenspor

Hal

et al. 2001

Physiological Genomics

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White (WAT) and brown (BAT) adipose tissue are tissues of energy storage and energy dissipation, respectively. Experimental evidence suggests that brown and white preadipocytes are differentially determined, but so far not much is known about the genetic control of this determination process. The aim of this study was to identify differentially expressed genes involved in brown and white preadipocyte development. Using representational difference analysis (cDNA RDA) and DNA microarray screening, we identified four genes with higher expression in white preadipocytes (three different complement factors and ␦-6 fatty acid desaturase) and seven genes with higher expression levels in brown preadipocytes, of which three are structural genes implicated in cell adhesion and cytoskeleton organization (fibronectin, ␣-actinin-4, metargidin) and four that might function in gene transcription and protein synthesis (vigilin, necdin, snRNP polypeptide A, and a homolog to human hepatocellular carcinomaassociated protein). The expression profile of these genes was analyzed during preadipocyte differentiation, upon ␤-adrenergic stimulation, and in WAT and BAT tissue in vivo compared with references genes such as peroxisome proliferatoractivated receptor-␥ (PPAR␥), uncoupling protein 1 (UCP1), cytochrome c oxidase. adipocyte differentiation; thermogenesis; preadipocyte marker genes; uncoupling protein; cDNA representational-difference analysis; DNA microarray analysis WHITE AND BROWN ADIPOSE TISSUES represent counter actors in energy partitioning, channeling lipid energy either to accumulation in white fat (WAT) or to oxidation, i.e., dissipation in brown fat (BAT) a highly thermogenic tissue (23). Throughout the last years considerable progress has been made in elucidating the molecular mechanisms of adipocyte differentiation which involves sequential activation of numerous transcription factors from several families like different members of the CCAAT/enhancer binding proteins (C/ EBP) and peroxisome proliferator-activated receptors (PPAR) (1,15,30,44,52). However, most of these studies focused on differentiation of white preadipocytes using established white preadipocyte cell lines such as 3T3-L1 and 3T3-F442A cells (37). One of the remaining questions is how and at which stage of development the differentiation of BAT vs. WAT is regulated, of which very little is currently known. Brown and white adipocytes show distinct morphological and biochemical phenotypes in vivo (9). When differentiated in vitro, brown adipocytes show a higher respiratory capacity than white adipocytes and express the BAT specific uncoupling protein 1 (UCP1), which is considered to be a marker for brown adipocytes (21). It is still not clear whether BAT and WAT derive from the same adipose precursor cells or arise independently from distinct mesenchymal stem cells (44), although recently PGC-1, a coactivator of PPAR␥, has been identified, which induces genes important in the development of brown adipocyte phenotype (41).We have performed parallel culture...

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Section: Generation Of a Cdna Library Of Candidate Genesmentioning

confidence: 99%

Differential gene expression in white and brown preadipocytes

Boeuf

Klingenspor

Hal

et al. 2001

Physiological Genomics

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“…The recently developed cDNA microarray technology enabled monitoring of cell-, tissue-and developmental stage-specific gene expression profiles and simultaneous quantitative analyses of expression levels of genes [15][16][17][18][19], which could help people to further find out new genes possibly involved in the same process or signaling pathway. This will help people to have the general and full knowledges on certain developmental processes.…”

Section: Introductionmentioning

confidence: 99%

Identification of ABA-responsive genes in rice shoots via cDNA macroarray

Lin

et al. 2003

Cell Res

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Phytohormone abscisic acid (ABA) was critical for many plant growth and developmental processes including seed maturation, germination and response to environmental factors. With the purpose to detect the possible ABA related signal transduction pathways, we tried to isolate ABA-regulated genes through cDNA macroarray technology using ABA-treated rice seedling as materials (under treatment for 2, 4, 8 and 12 h). Of 6144 cDNA clones tested, 37 differential clones showing induction or suppression for at least one time, were isolated. Of them 30 and 7 were up-or down-regulated respectively. Sequence analyses revealed that the putative encoded proteins were involved in different possible processes, including transcription, metabolism and resistance, photosynthesis, signal transduction, and seed maturation. 6 cDNA clones were found to encode proteins with unknown functions. Regulation by ABA of 7 selected clones relating to signal transduction or metabolism was confirmed by reverse transcription PCR. In addition, some clones were further shown to be regulated by other plant growth regulators including auxin and brassinosteroid, which, however, indicated the complicated interactions of plant hormones. Possible signal transduction pathways involved in ABA were discussed.

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“…T-DNA and transposon insertion mutagenesis (Feldmann, 1991;Tissier et al, 1999), the analysis of synteny between different plant species (Devos and Gale, 2000), the use of chimeraplasty to create specific mutations in plant genes (Beetham et al, 1999), and the introduction of activation tagging as a gain-offunction screen (Weigel et al, 2000) have already revealed new insights into the function of specific genes. Microarray tracking of global gene expression in a plant cell or tissue (Van Hal et al, 2000) and proteomic analysis of protein expression patterns (Thiellement et al, 1999) have evolved as additional powerful tools to draw a broader picture of how plants alter biochemical processes over time or in response to environmental stimuli. Furthermore, metabolomics provides complementary information from profiles of metabolites produced by various plants and plant tissues in response to change.…”

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confidence: 99%

Isoprenoid Biosynthesis. Metabolite Profiling of Peppermint Oil Gland Secretory Cells and Application to Herbicide Target Analysis

2001

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Two independent pathways operate in plants for the synthesis of isopentenyl diphosphate and dimethylallyl diphosphate, the central intermediates in the biosynthesis of all isoprenoids. The mevalonate pathway is present in the cytosol, whereas the recently discovered mevalonate-independent pathway is localized to plastids. We have used isolated peppermint (Mentha piperita) oil gland secretory cells as an experimental model system to study the effects of the herbicides fosmidomycin, phosphonothrixin, methyl viologen, benzyl viologen, clomazone, 2-(dimethylamino)ethyl diphosphate, alendronate, and pamidronate on the pools of metabolites related to monoterpene biosynthesis via the mevalonate-independent pathway. A newly developed isolation protocol for polar metabolites together with an improved separation and detection method based on liquid chromatography-mass spectrometry have allowed assessment of the enzyme targets for a number of these herbicides.The growing body of gene sequence information from a variety of plants, in combination with experimental genomics, is beginning to revolutionize the understanding of plant metabolism. These new technologies based on sequence information can be readily integrated with traditional biochemical and genetic approaches to add new dimensions to the study of complex metabolic pathways in plants.

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The application of DNA microarrays in gene expression analysis

Cited by 199 publications

References 39 publications

Differential gene expression in white and brown preadipocytes

Differential gene expression in white and brown preadipocytes

Identification of ABA-responsive genes in rice shoots via cDNA macroarray

Isoprenoid Biosynthesis. Metabolite Profiling of Peppermint Oil Gland Secretory Cells and Application to Herbicide Target Analysis

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