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publications by UHNMAC users: array-based applications
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The following lists contain selected publications on several of our service applications. For more publications, please visit here.

aCGH (6 publications)
Gerstein AC, et al. Ploidy reduction in Saccharomyces cerevisiae. Biol Lett 2008, 4:91-94

Using yeast arrays for aCGH, researchers investigated the mechanisms involved in ploidy reduction for Saccharomyces cerevisiae. The results of this study suggest the existence of a mitotic mechanism allowing the elimination of an entire set of chromosomes, thus reducing the ploidy level.

Iakovlev VV, et al. Genomics Differences Between Pure Ductal Carcinoma In Situ of the Breast and that Associated wih Invasive Disease: a Calibrated aCGH Study. Clin Cancer Res 2008, 14:4446

aCGH was used to compare the genomic alterations between ductal carcinoma in situ (DCIS) and DCIS with infiltrating duct carcinoma (IDC). This study found that gain on 17q22-24.2 was associated with higher histologic grade, large IDC size, lymphatic/vascular invasion, and lymph node metastasis (P < 0.05), and is a candidate region as a predictor of invasion in DCIS.

Ghazani AA, et al. Genomic Alterations in Sporadic Synchronous Primary Breast Cancer Using Array and Metaphase Comparative Genomic Hybridization. . Neoplasia 2007, 9(6):511

This study used aCGH and metaphase CGH to examine the genetic alterations of 23 synchronous breast cancers from 10 patients. When compared to their matched counterparts, synchronous breast cancers frequently had chromosomal gains of 1q, 3p, 4q, and 8q, and losses of 11q, 12q, 16q, and 17p. Copy number amplification of 1p31.3-1p32.3 (which harbours JAK1) was present in all tumour samples.

Pandita A, et al. Malignant and benign ganglioglioma: A pathological and molecular study. Neuro Oncol, 2007, 9(2):124

This molecular-pathological study provides insight into the pathogenesis of gangliogliomas and associated rare malignant progression. aCGH analyses using Human 19K cDNA arrays found chromosomal losses to be predominant in the benign areas of the ganglioglioma, with gains more prevalent in the malignant component. Direct analysis demonstrated loss of p19 expression and p53 mutation in the malignant areas, highly suggestive of these alterations being involved in the malignant progression of the ganglioglioma.

Gerstein AC, et al. Genomic Convergence toward Diploidy in Saccharomyces cerevisiae. PLoS Genet, 2006, 2(9):e145

Using Yeast 6.4K ORF arrays, researchers used aCGH to investigate genome size evolution in haploid, diploid, and tetraploid initially isogenic lines of the yeast Saccharomyces cerevisiae. Over the course of ~1,800 generations of mitotic division, and in both stressful and unstressful environments, convergence toward diploid DNA content in all replicate lines was observed.

Ghazani AA, et al. Limited tissue fixation times and whole genome amplification do not impact array CGH profiles. J Clin Pathol 2006, 59:311-315

This study investigates the suitability and integrity of the DNA extracted from formalin fixed, paraffin embedded (FFPE) MCF7 breast cancer cells for aCGH applications. Similar profiles between FFPE MCF7 cells and their fresh counterpart and between amplified and non-amplified FFPE MCF7 cells were observed. This study used Human 19K and 1.7K arrays.

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ChiP-on-Chip: Human CGI and Yeast ORF arrays (8 publications)
Human CGI arrays

Frontini M, et al. A ChIP-chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response. Nuc Acids Res 2009, 37(4):1073

Using ChIP-chip (HCGI12K arrays), 202 new binding sites were identified for the transcription factor IRF1. Although previously found to regulate key processes in the immune system and in tumor suppression, IRF1 was also found to be involved in the interstrand crosslink (ICL) DNA damage response pathway.

Hoemme C, et al. Chromatin modifications induced by PML-RARα repress targets in leukemogenesis as analyzed by ChIP-Chip. Blood, 2008, 111:2887

Using ChIP-chip (HCGI 12K arrays), 372 direct genomic PML-RAR targets, including regulators of global transcriptional programs and critical regulatory genes for cell-cycle control and apoptosis, were identified. The binding of PML-RAR to target promoters and the resulting histone modifications resulted in mRNA repression of functionally relevant genes. This study concludes that the transcription factor PML-RAR regulates key cancer-related genes.

Huang W, et al. The Interferon Consensus Sequence-binding Protein (ICSBP/IRF8) Represses PTPN13 Gene Transcription in Differentiating Myeloid Cells. Biol Chem 2008, 283(12):7921-35

CGI arrays were screened with chromatin that co-immunoprecipitated with interferon consensus sequence-binding protein (ICSBP/IRF8) in order to identify ICSBP target genes. Using this technique, we identified PTPN1, which encodes Fas-associated phosphatase 1 (a ubiquitously expressed protein-tyrosine phosphatase), as an ICSBP target gene. This study identified a mechanism for increased survival of mature myeloid cells in the ICSBP-deficient murine model and in human myeloid malignancies with decreased ICSBP expression.

Miao F, et al. Histone Methylation Patterns Are Cell-Type Specific in Human Monocytes and Lymphocytes and Well Maintained at Core Genes. J Immunology 2008, 180:2264-2269

Researchers used ChIP combined with microarrays to map histone H3K9 dimethylation (H3K9Me2) patterns in gene coding and CGI regions in human monocytes and lymphocytes. The results of this study demonstrate that monocytes and lymphocytes have distinct epigenomes and that H3K9Me2 may have a role in the regulation of genes required for immune response and cell-type specificity.

Ponzielli R, et al. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res. 2008, 36(21):e144

This study is the first to provide a comprehensive evaluation of experimental ChIP-chip design parameters. Parameters specific to ChIP-chip, such as antibody purity, amplification method for enriched DNA, and the array hybridization control were evaluated, in addition to parameters previously evaluated for gene expression studies.

Zhang Y, et al. Identification and characterization of CCAAT/Enhancer Binding proteinδ (C/EBPδ) target genes in G0 growth arrested mammary epithelial cells. BMC Mol Biol 2008, 9:83

CCAAT/Enhancer Binding Proteinδ (C/EBPδ) target genes were identified using ChIP-chip. The identification and validation of such target genes provides new insight into the role of C/EBPδ in mammary epithelial cell biology.

Wu J, et al. Diverse histone modifications on histone 3 lysine 9 and their relation to DNA methylation in specifying gene silencing.. BMC Genomics 2007, 8:131

Using ChIP-chip, histone modifications acetyl-H3K9 and dimethyl-H3K9 were profiled in the mouse leukemia cell line L1210. This study found that acetyl-H3K9 shows an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing, and that dimethyl-H3K9 appears to be less distinct in relation to promoter methylation.

Yeast ORF arrays

Schafer G, et al. The Saccharomyces cerevisiae linker histone Hh01p is essential for chromatin compaction in stationary phase and is displaced by transcription. PNAS 2008, 105(39):14838

Using Yeast 6.4K arrays, Schafer et al. investigated the role of the linker histone H1 in S. cerevisiae and conclude that linker histone Hho1p has a limited role in transcriptional regulation.

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DNA Methylation: Human and Mouse CGI arrays (9 publications)
Human CGI arrays

Kaminsky ZA, Tang T, Wang S-C, et al. DNA methylation profiles of monozygotic and dizygotic twins. Nature Genetics 2009, 41:240

Using HCGI 12K arrays for methylation profiling, this study investigated the epigenetic variation among monozygotic twins and the epigenetic similarity between monozygotic and dizygotic twins. The results indicate that the epigenetic similarity in monozygotic twins was more highly conserved in regulatory regions of the genome, suggesting a functional stratification of the epigenome.

Kaminsky Z, et al. Epigenetics of personality traits: an illustrative study of identical twins discordant for risk-taking behavior. Twin Res Hum Genet. 2008 11(1):1

HCGI12K arrays were used to identify DNA methylation differences between phenotypically discordant identical twins. This study found that differential methylation of CpG islands proximal to the homeobox DLX1 gene could modulate stress responses and risk taking behaviour.

Lai HC, et al. Identification of novel DNA methylation markers in cervical cancer. Int J Cancer. 2008, 123(1):161

The aim of this study was to identify novel genes that are methylated in cervical cancers and to test their potential in clinical applications. Using CGI arrays to uncover methylated genes in squamous cell carcinomas (SCC) of the uterine cervix, researchers reported 6 genes (SOX1, PAX1, LMX1A, NKX6-1, WT1 and ONECUT1) more frequently methylated in SCC tissues than in their normal controls. These novel DNA methylations may be a promising approach for the screening of cervical cancers.

Mill J, et al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet. 2008 Mar; 82(3):696

Researchers identified DNA-methylation changes in the frontal cortex and germline associated with schizophrenia and bipolar disorder. This study found evidence for psychosis-associated DNA methylation differences in numerous loci (including brain development and neurotransmission) and evidence for a strong correlation between DNA methylation in the MEK1 gene promoter region and lifetime antipsychotic use in schizophrenia patients.

Onken MD, et al. A Metastasis Modifier Locus on Human Chromosome 8p in Uveal Melanoma Identified by Integrative Genomic Analysis. Clin Cancer Res 2008, 14(12):3737

The purpose of this study was to identify genes that modify metastatic risk in uveal melanoma, a type of cancer that has a consistent metastatic pattern. Using integrative genomic methods, including gene expression profiling, aCGH, differential hybridisation methylation, and SNP-based detection of loss of heterozygosity, this study found a candidate gene, leucine zipper tumor suppressor-1 (LZTS1), located in chromosome region 8p12-22, strongly linked to rapid metastasis.

Estécio MRH, et al. High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res, 2007, 17:1529

Researchers present an improved method to identify methylated genes genome-wide by hybridising a CpG island microarray with amplicons obtained by the methylated CpG island amplification technique. This method was validated in three cancer cell lines and 15 primary colorectal tumours, resulting in the discovery of hundreds of new methylated genes in cancer.

Ho S, Tang W. Techniques used in studies of epigenome dysregulation due to aberrant DNA methylation: An emphasis on fetal-based adult diseases. Reprod Toxicol, 2007, 23(3):267

A review of existing and emerging technologies used in studying DNA methylation including methylation sensitive restriction fingerprinting (MSRF), restriction landmark genomic scanning (RLGS), methylation CpG island amplification-representational difference analysis (MCA-RDA), differential methylation hybridisation (DMH), and cDNA microarrays combined with treatment with demethylating agents and inhibitors of histone deacetylase.

Mouse CGI arrays

Gowher H, et al. Vezf1 regulates genomic DNA methylation through its effects on expression of DNA methyltransferase Dnmt3b. Genes Dev 2008, 22:2075

Using MCGI 4.6K arrays, Gowher et al report that mouse embryonic stem cell line deletion of vascular endothelial zinc finger 1 (Vezf1) results in loss of DNA methylation throughout the genome due to a decrease in the abundance of the de novo DNA methyltransferase, Dnmt3b. This result suggests that Vezf1 mutations may have widespread effects on the epigenetic regulation of gene expression.

Novikova SI, et al. Maternal Cocaine Administration in Mice Alters DNA Methylation and Gene Expression in Hippocampal Neurons of Neonatal and Prepubertal Offspring. PLoS ONE 2008, 3(4):e1919

Using MCGI 7.3K arrays, the hypothesis that maternal cocaine exposure could alter the fetal epigenetic machinery sufficiently to cause lasting neurochemical and functional changes in the offspring was tested. Following maternal cocaine exposure, global DNA methylation was profiled in offspring at 3 (P3) and 30 (P30) days postnatum. By P30, some cocaine-associated effects at P3 endured, reversed to opposite directions, or disappeared, and additional sets of abnormally methylated targets emerged at P30 that were not observed at P3.

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Gene Expression: Human cDNA arrays (22 publications)
Bane AL, et al. Expression profiling of familial breast cancers demonstrates higher expression of FGFR2 in BRCA2-associated tumors. Breast Cancer Res Treat 2009, 117(1):183

Using Human 19k arrays, Bane et al. profiled breast tumour RNA from BRCA1 and BRCA2 mutation carriers. The results of this study found that BRCA1-associated tumours had increased expression of component genes of the Notch and TGFbeta pathways and BRCA2-associated tumours had higher expression of FGFR2 and FGF1.

Behera RK, Nayak R. Expression Profiling of Nucleotide Metabolism-Related Genes in Human Breast Cancer Cells After Treatement wih 5-Fluorouracil. Cancer Investigation 2009, 27(5):561

The goal of this study was to determine the number of nucleotide metabolism genes regulated by 5-fluorouracil (5-FU), a widely used cancer drug, in the MCF-7 breast cancer cell line. This study identified novel genes, such as thioredoxin reductase, ectonucleotide triphosphate dephosphorylase, and CTP synthase, that are regulated by 5-FU, and revealed differentially expressed genes not involved directly in the known mechanism of action of 5-FU.

Hussein S, et al. Characterization of humam septic sera induced gene expression modulation in human myocytes. Int J Clin Exp Med 2009, 2:131-148

The Human 1.7k array was used to profile the gene expression of cultured human fetal cardiac myocytes with either 10% sera from septic patients or 10% sera from healthy volunteers. The septic sera resulted in the down-regulation of 178 genes and led to cell cycle, metabolic, transcription factor and apoptotic gene expression changes.

Peterkova M, et al. Microarray Analysis Using a Limited Amount of Cells. Folia Biologica (Praha) 2009, 55:53-60

This study evaluated various RNA isolation and amplfication methods in order to obtain enough input RNA for microarray experiments from small samples. The study found that the combination of RNAqueous(TM) Kit (Ambion) and SenseAmp Plus Kit (Genisphere) produced the best results following microarray experiments using the Hum19k array.

Purbey PK, et al. Acetylation-Dependent Interaction of SATB1 and CtBP1 Mediates Transcriptional Repression by SATB1. Mol Cell Biol 2009, 29(5):1321

Special AT-rich binding protein 1 (SATB1) is a global regulator of gene expression that acts predominantly as a repressor via the recruitment of histone deacetylase 1 (HDAC1) complexes. This study has found that SATB1 and C-terminal binding protein 1 (CtBP1) form a repressor complex in vivo. Gene expression studies using cells in which both SATB1 and CtBP1 were silenced have indicated commonly targeted genes that could be coordinately repressed by the SATB1-CtBP1 complex.

Veitch ZW, et al. Induction of 1C aldoketoreductases and other drug dose-dependent genes upon acquisition of anthracycline resistance. Pharmacogenet Genomics 2009,19(6):477

This study used microarrays and qPCR to identify genes whose expression can be correlated with the onset and/or magnitude of anthracycline resistance in breast tumour cells. The genes identified included the redox genes AKR1C2 and AKR1C3, in addition to genes associated with drug transport, cell signalling, cell proliferation or apoptosis, and protection from reactive oxygen species.

Anraku M, et al. Impact of Human Donor Lung Gene Expression Profiles on Survival after Lung Transplantation: A Case-Control Study. Am J of Transplantation 2008, 8(10):2140

This study identified the distinctive donor lung gene expression signature associated with primary graft dysfunction, a major cause of death after lung transplantation.

Borland MK, et al. Chronic, low-dose rotenone reproduces Lewy neurites found in early stages of Parkinson's disease, reduces mitochondrial movement and slowly kills differentiated SH-SY5Y neural cells. Mol Neurodegeneration 2008, 3:21

In this study, a differentiation protocol for human SH-SY5Y neuroblastoma that yielded non-dividing dopaminergic neural cells was developed. Following exposure to rotenone, a complex I inhibitor used in Parkinson's disease models, transcript expression was profiled using Human 19K cDNA arrays.

Camats M, et al. P68 RNA Helicase (DDX5) Alters Activity of Cis- and Trans-Acting Factors of the Alternative Splicing of H-Ras. PloS ONE 2008, 3(8):e2926

Using Human 19K cDNA arrays, researchers profile the gene expression of several knockdown models (including the knockdown of hnRNP A1, FUS/TLS and hnRNP H) to further investigate the role of p68 RNA helicase in the regulation of H-Ras expression and a vital transduction signal pathway linked to cell proliferation.

Chen L, et al. Gene expression profiling of early primary biliary cirrhosis: possible insights into the mechanism of action of ursodeoxycholic acid. Liver International, 2008, 28(7):997

Gene expression profiling using Human 19K cDNA arrays was performed to compare liver tissue from patients with primary biliary cirrhosis (treatment-naïve and ursodeoxycholic acid (UDCA)-treated patients). This study found that the effects of UDCA are mediated, at least in part, via a modulation of protein biosynthetic pathways.

Flatscher-Bader T, et al. Smoking and alcoholism target genes associated with plasticity and glutamate transmission in the human ventral tegmental area. Hum Mol Genet 2008, 17(1):38-51

This study utilised Human 19K cDNA arrays to identify genes sensitive to chronic alcohol abuse and smoking. This study, which found smoking induced the expression levels of vesicular glutamate transporters SLC17A6 and SLC17A7, concluded that plasticity within the VTA may be a molecular mechanism for the maintenance of smoking addiction and that alcohol, nicotine and co-abuse have distinct impacts on glutamatergic transmission.

Hauck TS, et al. Assessing the Effect of Surface Chemistry on Gold Nanorod Uptake, Toxicity, and Gene Expression in Mammalian Cells. Small 2008, 4(1):153

Human 10K cDNA arrays were used to examine the molecular changes of cells exposed to gold nanorods coated with polydiallyldimethylammonium chloride (PDADMAC). The finding that these nanorods have negligible impact on cell function suggests the nanorods are well suited for therapeutic applications, such as thermal cancer therapy, due to their tunable cell uptake and low toxicity.

Prasher B, et al. Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda. J Translational Medicine 2008, 6(48)

This article discusses Ayurveda, an ancient system of personalised medicine practiced in India since 1500 B.C., and whether the different constitution types described in Ayurveda have molecular correlates. This is a first attempt at integrating the clinical phenotyping principle of a traditional system of medicine with modern biology.

Wong V, et al. The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers. BMC Cancer 2008, 8:277

In order to examine a critical variable in DNA microarray experimentation, the timing of tissue acquisition, Wong et al compared the expression data from biospecimens taken in vivo and ex vivo. The data shows that FOS-related genes, which have been associated with hypoxia and breast cancer development, were differentially expressed before and after surgery.

Bianchini M, et al. cDNA microarray study to identify expression changes relevant for apoptosis in K562 cells co-treated with amifostine and imatinib. Cancer Chemotherapy and Pharmacology, 2007, 59(3): 349-360

Using Human 19K arrays for transcriptional profiling of cells treated with amifostine and imatinib (treatment for leukemia), researchers were able to identify a transcriptional repressor of survival genes that could potentially be helpful to overcome imatinib resistance. This study demonstrates the importance of in vitro testing of a novel drug combination most likely to predict its potential usefulness for in vivo application.

Cameron MJ, et al. Interferon- Mediated Immunopathological Events Are Associated with Atypical Innate and Adaptive Immune Responses in Patients with Severe Acute Respiratory Syndrome. J Virol, 2007, 81(16):8692

Researchers use gene expression signatures of patients with severe acute respiratory syndrome (SARS) to analyse host innate and adaptive immune responses during discrete phases of illness. A novel signature of high interferon (IFN)- , IFN- , and IFN-stimulated chemokine levels, plus robust antiviral IFN-stimulated gene (ISG) expression, accompanied early SARS sequelae.

Chattopadhyay I, et al. Gene expression profile of esophageal cancer in North East India by cDNA microarray analysis. World J Gastroenterol 2007, 13(9):1438

This study has identified differential gene expression in tumors isolated from patients with esophageal cancer. Most significantly upregulated genes were involved with the MAPK pathway, G-protein coupled receptor family, ion transport, and serine or threonine kinase activity, and most downregulated genes were involved with ribosome structure, endopeptidase inhibitor activity, cytoskeleton structure, antioxidant activity, acyl group transferase activity, and translation elongation factor activity. Several altered genes were also reported from a high incidence area of esophageal cancer in China.

Gilbert I, et al. A molecular analysis of the population of mRNA in bovine spermatozoa. Reproduction 2007, 133:1073

Researchers address the possible functional role for RNA transcripts present in spermatozoa, which are generally considered to be remnants of spermiogenesis. This study indicates that the sperm transcriptome harbors a complex mixture of messengers implicated in a wide array of cell functions and suggest that sperm RNA profiling could allow the molecular diagnosis of male gamete quality.

Haque T,et al. Gene Expression Profiling from Formalin-Fixed Parrafin-Embedded Tumors of Pediatric Glioblastoma. Clin Cancer Res 2007, 13(21):6284

This study found that gene expression profiling using archived formalin-fixed, paraffin-embedded tissue sample was possible in most (16 of 19) test samples and that the expression pattern was similar to that of fresh frozen samples.

Panigrahi P, et al. Probiotic bacteria change Escherichia coli-induced gene expression in cultured colonocytes: Implications in intestinal pathophysiology. World J Gastroenterol, 2007, 13(47):6370

This study used Human 19K cDNA microarrays to examine the expression profile of Caco-2 cells infected with strains of normal E. coli and Lactobacillus plantarum. The study concludes that commensal bacterial strains induced the expression of genes involved in important cellular processes, including regulation of transcription, protein biosynthesis, metabolism, cell adhesion, and apoptosis, and that such changes may influence physiologic and pathologic responses in the host.

Siriwardhana N, Wang H-CR.Precancerous carcinogenesis of human breast epithelial cells by chronic exposure to benzo[a]pyrene. Mol Carcinogenesis, 2007, 47(5):338

The molecular changes involved in the carcinogenesis of human breast epithelial cells induced by exposure to benzo[a]pyrene was studied to understand the effects of chronic exposure to environmental pollutants. Using Human 19K cDNA microarrays, researchers detected seven genes related to human cancers in B[a]P-transformed breast epithelial cells. In addition, this study verified that green tea catechin significantly suppressed B[a]P-induced carcinogensis.

Wong WW-L, et al. Determinants of sensitivity to lovastatin-induced apoptosis in multiple myeloma. Mol Cancer Therapeutics, 2007, 6:1886

Statins, commonly used to treat hypercholesterolemia, have the ability to trigger tumour-specific apoptosis in certain cancers including multiple myeloma (MM). This study shows that of a panel of 17 genetically distinct MM cell lines, half were sensitive to statin-induced apoptosis and, despite pharmacodynamic evidence of drug uptake and activity, the remainder was insensitive. This suggests that statins trigger apoptosis by blocking many signaling cascades, directly or indirectly deregulated by the oncogenic lesions of the tumour cell.

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Gene Expression: Yeast ORF arrays (10 publications)
Marin MJ, et al. Different modulation of the outputs of yeast MAPK-mediated pathways by distinct stimuli and isoforms of the dual-specificity phophastase Msg5. Mol Genet Genomics 2009, 281(3):345

The Yeast 6.4k arrays were used to compare the expression profile of an msg5 mutant to that of the isogenic wild type strain during vegetative growth. When analysing the impact of Msg5, this study found that both Msg5 isoforms interact similarly with Slt2, whereas the long form binds Fus3 with higher affinity.

Molin C, et al. mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress. RNA 2009, 15:600

This study investigates mRNA turnover rates and mRNA steady-state levels following hyperosmotic shock in S. cerevisiae cells. The MAP kinase Hog1 affects both steady-state levels and stability of stress-responsive transcripts, whereas the Hog1-activated kinase Rck2 influences steady-state levels without a major effect on stability. The study concludes that mRNA turnover is coordinated with transcriptional induction.

Cui Y, et al. Genome wide expression analysis of the CCR4-NOT complex indicates that it consists of three modules with the NOT module controlling SAGA-responsive genes. Mol Genetics and Genomics 2008, 279(4):323-337

Using deletions in seven of the CCR4-NOT genes, researchers used whole genome microarray analysis to determine the overall mRNA expression patterns that are affected by members of the yeast CCR4-NOT complex. The results of the study indicate that distinct portions of the CCR4-NOT complex control a number of cellular processes. Microarray analysis indicated that BTT1 and CAF130 correlate very highly in their control of gene expression and preferentially repress genes involved in ribosome biogenesis.

Hausmann A, et al. Cellular and Mitochondrial Remodeling upon Defects in Iron-Sulfur Protein Biogenesis. J Biol Chem, 2008, 283(13):8318

This study compared the global transcriptional responses to defects in three biogenesis systems in S. cerevisiae to define the integration of iron-sulfur biogenesis into cellular homeostasis. The results of the differential gene expression analysis indicated that mitochondria and their ISC systems serve as global regulators in iron-dependent processes.

Ilina Y, et al. Characterization of the DNA binding motif of the arsenic-responsive transcription factor Yap8p. Biochem J, 2008, Jun 26 [Epub ahead of print]

Using the Yeast 6.4K array, researchers determined the principal function of Yap8p, an AP-1-like transcription factor, is to control expression of ACR2 (arsenate reductase) and ACR3 (arsenite efflux protein) expression in response to arsenic. This study also characterised the DNA sequence targeted by Yap8p, a pseudo-palindromic sequence that is related to but distinct from the sequence recognised by other fungal AP-1 proteins.

Schäfer G, et al. The Saccharomyces cerevisiae linker histone Hh01p is essential for chromatin compaction in stationary phase and is displaced by transcription. PNAS 2008, 105(39):14838

This investigation found a genome-wide anticorrelation between the level of bound linker histone Hho1p and gene expression in S. cerevisiae. Despite the importance of core histones in transcriptional regulation, this study suggests that Hho1p has only a limited role in transcriptional regulation.

Abruzzi K, et al. A Novel Plasmid-Based Microarray Screen Identifies Suppressors of rrp6∆ in Saccaromyces cerevisiae. Mol Cell Biol, 2007, 27(3):1044-1055

To find suppressor genes in yeast, this study compares a traditional plate screen and a novel microarray enhancer/suppressor screening (MES) strategy. Both screening methods identified overlapping, but also different, suppressor genes. Only MES identified the novel mRNP protein Nab6p and the tRNA transporter Los1p, which could not have been identified in a traditional plate screen; both genes are toxic when overexpressed in rrp6 strains at 37°C.

Hickman MJ & Winston F. Heme Levels Switch the Function of Hap1 of Saccharomyces cerevisae between Transcriptional Activator and Transcriptional Repressor. Mol Cell Biol, 2007, 27(21):7414

This study found that Hap1, originally identified as a heme-dependent transcriptional activator, can also act as a repressor of three ERG genes under hypoxic conditions. The data found that Hap1 binds to ERG gene promotors while other experiments indicated that a corepressor (Tup1/Ssn6) is also required for repression.

Joseph-Strauss D, et al. Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks. Genome Biology 2007, 8:R241

Using Yeast 6.4K arrays, researchers used expression profiling to follow the progression of spore germination and divide this process into two major stages; one in which spores respond only to glucose and the second in which cells respond to other nutritional components in the environment. Components of the mitotic cell cycle machinery are involved in spore germination but in a distinct pattern.

Koren A, et al. Autocorrelation analysis reveals widespread spatial biases in microarray experiments. BMC Genomics 2007, 8:164

Researchers conclude that spatial biases comprise a major source of noise in microarray studies and demonstrate the utility of autocorrelation analysis for the efficient identification and filtering of spurious chromosomal-position- dependent correlations. This study suggests that such biases may generate more than 15% false data per experiment. Computer simulations have shown that large spatial biases caused in the microarray hybridisation step can account for the observed spurious correlations, in contrast to previous suggestions

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Gene Expression: Mouse cDNA arrays (8 publications)
Hill JJ, et al. Glycoproteomic analysis of two mouse mammary cell lines during transforming growth factor (TGF)-β induced epithelial to mesenchymal transition. Proteome Science 2009, 7:2

This study used proteomic approaches to find proteins that change in abundance upon the induction of epithelial-to-mesenchymal transition (EMT) by TGF-β in two mouse mammary epithelial cell lines. Cell adhesion molecules and regulators of cell signalling were among the proteins that were modulated during the EMT process. Mouse 15K cDNA arrays were used to validate the proteomic data.

Penaloza C, et al. Sex of the cell dictates its response: differential gene expression and sensitivity to cell death inducing stress in male and female cells. FASEB J 2009, 23(6):1869

By profiling the gene expression of mice at three points in their development (embryos before sexual differentiation, embryos after the first assertion of sex hormones, and pubescent mice), this study concluded that cells differ innately according to sex irrespective of their history to sex hormones. These differences may have consequences in the course of sexually dimorphic diseases and their therapy.

Gerbe F, et al. Dynamic expression of Lrp2 pathway members reveals progressive epithelial differentiation of primitive endoderm in mouse blastocyst. Dev Biol 2008, 313:594

This study used a microarray strategy (involving Mouse 15K cDNA arrays) that combines transcriptome analysis of three stem cell lines and early embryos to isolate Lrp2 as a novel primitive endoderm precursor marker.

Marquis J-F, et al. Fibrotic Response as a Distinguishing Feature of Resistance and Susceptibility to Pulmonary Infection with Mycobacterium tuberculosis in Mice. Infect Immun 2008, 76(1):78

This study, which investigated the differential susceptibilty of DBA/2J (susceptible) and C57BL/6J (resistant) mouse strains to pulmonary tuberculosis, found that significant differentially expressed genes were associated with tissue remodeling and the fibrotic response.

Mamane Y, et al. Epigenetic Activation of a Subset of mRNAs by eIF4E Explains Its Effects on Cell Proliferation. PLoS ONE, 2007, 2(2):e242

The induction of eIF4E, an mRNA 5’ cap-binding protein, resulted in increased translation of specific mRNAs, including those that encode anti- apoptotic proteins and cell growth-related factors. By studying mRNA targets that are translationally responsive eIF4E, researchers were able to shed new light on the mechanisms by which eIF4E prevents apoptosis and transforms cells.

Yu Y, et al. Influence of murine maternal diabetes on placental morphology, gene expression, and function. Archives of Physiology and Biochemistry 2008, 114(2):99

Using Mouse 15K cDNA arrays, Yu et al investigate the mRNA expression of diabetic mouse placentas and control placentas. Most of the differentially expressed genes identified are involved in metabolism, immunity and defence, and signal transduction.

Karar J, et al. Expression and functional activity of prooxidant and antioxidants in murine heart exposed to acute hypobaric hypoxia. FEBS Letters 2007, 581(24):4577

Using Mouse 15k cDNA arrays, this study provides insight on the cellular antioxidant defence mechanisms in murine heart under acute hypobaric hypoxia. Interestingly, a decrease in the protein level of Cyba, a subunit of NADPH oxidase (a major ROS generator in the heart) was found in AHH exposed heart.

Prasanna SJ, et al. Involvement of oxidative and nitrosative stress in modulation of gene expression and functional responses by IFN-γ. International Immunology, 2007, 19(7):867

Mouse 15K cDNA arrays were used to screen a mouse hepatoma cell line for IFN -modulated genes. This study revealed modulation of genes involved in oxidative and nitrosative stress (iNos, gp91phox and Catalase) and increased generation of reactive oxygen species (ROS) and reactive nitrogen intermediates (RNIs) upon IFN treatment. IFN -modulated genes can be categorised into two distincit sets: oxidative and nitrosative stress independent (transporter associated with antigen processing 2, Cd80, Lmp10 and Icosl) and oxidative and nitrosative stress dependent (iNos, gp91phox, Catalase and Id2).

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Gene Expression: Immunarray (1 publication)
Baron C, et al. Prediction of Graft-Versus-Host Disease in Humans by Donor Gene-Expression Profiling. PLoS Med, 2007, 4(1):e23

By measuring the expression profiles of CD4+ and CD8+T cells from allogeneic hematopoietic cell transplantation (AHCT) donors, researchers tested the hypothesis that some donors may be “stronger alloresponders” than others, and consequently more likely to elicit graft-versus-host disease (GVHD). This study finds that pre-AHCT profiling segregates donors whose recipient suffered from GVHD or not and concludes that the ability to discriminate strong and weak alloresponders could pave the way to personalised transplantation medicine.

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Gene Expression: Custom arrays (1 publication)
Golkari S, et al. Microarray analysis of Fusarium graminearum-induced wheat genes: identification of organ- specific and differentially expressed genes. Plant Biotechnol J, 2007, 5(1):38-49

This study investigated the transcriptome patterns of six organs (glume, lemma, palea, anther, ovary and rachis) dissected from infected wheat spikes after inoculation with the fungus Fusarium graminearum, the causal agent of fusarium head blight disease. Using custom-printed wheat cDNA arrays, researchers learned that each organ had a defined and distinctive profile in response to the fungal infection and they were able to uncover new up- regulated genes expressed in specific organs.

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