Genome-wide expression monitoring in Saccharomyces cerevisiae

Wodicka, Lisa; Dong, Helin; Mittmann, Michael; Ho, Ming-Hsiu; Lockhart, David J.

doi:10.1038/nbt1297-1359

Cited by 920 publications

(611 citation statements)

References 42 publications

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“…19 The processing and scaling of the hybridization data were also performed as described previously. 20,21 Gene expression was quantitated in relative intensity units, and divided into three groups: low (o300), moderate (300-999) and high (Z1000).…”

Section: Oligonucleotide Microarraymentioning

confidence: 99%

Comprehensive analysis of HE4 expression in normal and malignant human tissues

2006

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The HE4 (WFDC2) gene encodes a WAP-type four disulphide core domain-containing protein with a presumptive role in natural immunity. Multiple studies have consistently identified upregulation of HE4 gene expression in carcinomas of the ovary; however, the expression in normal and malignant adult tissues has not been examined in detail. Here, we examined the expression of the HE4 gene and protein in a large series of normal and malignant adult tissues by oligonucleotide microarray and tissue microarray, respectively. HE4 gene expression was highest in normal human trachea and salivary gland, and to a lesser extent, lung, prostate, pituitary gland, thyroid, and kidney. In a series of 175 human adult tumors, gene expression was highest in ovarian serous carcinomas. However, adenocarcinomas of the lung, and occasional breast, transitional cell and pancreatic carcinomas had moderate or high levels of HE4 expression. Using tissue microarrays and full tissue sections of normal and 448 neoplastic tissues, HE4 immunoreactivity was found in normal glandular epithelium of the female genital tract and breast, the epididymis and vas deferens, respiratory epithelium, distal renal tubules, colonic mucosa, and salivary glands, consistent with HE4 gene expression. In addition to consistent positivity in ovarian carcinoma, some pulmonary, endometrial, and breast adenocarcinomas, mesotheliomas, and less often, gastrointestinal, renal and transitional cell carcinomas were also positive. Knowledge of the expression patterns of HE4 in our survey is useful for application in histopathologic diagnosis, and should be taken into consideration in future studies that examine the role of HE4 as a serological tumor biomarker or as a target for gene-based therapy.

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Section: Oligonucleotide Microarraymentioning

confidence: 99%

Comprehensive analysis of HE4 expression in normal and malignant human tissues

2006

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“…The samples were normalized using the total average difference between the perfectly matched probes and the mismatched probes. It has been reported that differences in hybridization intensity between the same ORFs on corresponding chips are proportional to changes in RNA levels (Wodicka et al, 1997) In this study we used only 4977 ORFs showing mRNA concentration above 100 units of hybridization intensity in the wild-type (wt) and the two mutants. The basic statistics of the ORFs used and the mRNA concentration in the three strains are given in Table 1.…”

Section: Genechip Expression Analysismentioning

confidence: 99%

Relationship between G+C content, ORF‐length and mRNA concentration in Saccharomyces cerevisiae

Marı́n

Gallardo

Kato

et al. 2003

Yeast

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RNA biogenesis is a tightly-regulated process. The levels and timing of expression of a gene depends on its particular function. However, gene expression levels may also depend on structural features. Here we describe the analysis of gene expression of 4977 ORFs using DNA microarrays covering the whole genome of three different S. cerevisiae strains, wild-type and tho2 and thp1 mutants with a general effect on mRNA biogenesis. We show that transcripts from G+C-rich ORFs accumulate at higher concentrations than those from G+C-poor ones, in different ORF-length categories in all strains tested. In addition, we found a negative correlation between ORF length and G+C content. Our results indicate that length and G+C content of a gene have a clear effect on its levels of expression. We discuss the biological relevance of these results, as well as different ways that these structural features could modulate mRNA biogenesis.

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“…RNA was isolated by the FastRNA kit-RED (BIO101), according to manufacturer's recommendation. A ymetrix oligonucleotide arrays, capable of detecting the entire ORF of the yeast genome (Ye6100) were used for mRNA expression pro®ling (Lockhart et al, 1996;Wodicka et al, 1997), as detailed previously . RNA abundance was determined based on the average of the di erences between perfect match and mismatch intensities for each probe family.…”

Section: Ubiquitin Labeling and Ub Ligation Assaymentioning

confidence: 99%

Yeast homolog of human SAG/ROC2/Rbx2/Hrt2 is essential for cell growth, but not for germination: chip profiling implicates its role in cell cycle regulation

Swaroop¹,

Wang²,

Miller³

et al. 2000

Oncogene

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In an attempt to understand the signaling pathway mediating redox-induced apoptosis, we cloned SAG, an evolutionarily conserved zinc RING ®nger gene that, when overexpressed, protects cells from apoptosis induced by redox agents. Here we report functional characterization of SAG by the use of yeast genetics approach. Targeted disruption of ySAG, yeast homolog of human SAG, and subsequent tetrad analysis revealed that ySAG is required for yeast viability. Complementation experiment showed that the lethal phenotype induced by the ySAG deletion is fully rescued by wildtype SAG, but not by several hSAG mutants. Complementation experiment has also con®rmed that ySAG is essential for normal vegetative growth, rather than being required for sporulation. Furthermore, cell death induced by SAG deletion was accompanied by cell enlargement and abnormal cell cycle pro®ling with an increased DNA content. Importantly, SAG was found to be the second family member of Rbx (RING box protein) or ROC (Regulator of cullins) or Hrt that is a component of SCF E3 ubiquitin ligase. Indeed, like ROC1/Rbx1/Hrt1, SAG binds to Cul1 and SAG-Cul1 complex has ubiquitin ligase activity to promote poly-ubiquitination of E2/ Cdc34. This ligase activity is required for complementation of death phenotype induced by ySAG disruption. Finally, chip pro®ling of the entire yeast genome revealed induction of several G1/S as well as G2/M checkpoint control genes upon SAG withdrawal. Thus, SAG appears to control cell cycle progression in yeast by promoting ubiquitination and degradation of cell cycle regulatory proteins.

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Genome-wide expression monitoring in Saccharomyces cerevisiae

Cited by 920 publications

References 42 publications

Comprehensive analysis of HE4 expression in normal and malignant human tissues

Comprehensive analysis of HE4 expression in normal and malignant human tissues

Relationship between G+C content, ORF‐length and mRNA concentration in Saccharomyces cerevisiae

Yeast homolog of human SAG/ROC2/Rbx2/Hrt2 is essential for cell growth, but not for germination: chip profiling implicates its role in cell cycle regulation

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