TITLE

Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays

AUTHOR(S)
Adjaye, James; Herwig, Ralf; Herrmann, Doris; Wruck, Wasco; BenKahla, Alia; Brink, Thore C.; Nowak, Monika; Carnwath, Joseph W.; Hultschig, Claus; Niemann, Heiner; Lehrach, Hans
PUB. DATE
January 2004
SOURCE
BMC Genomics;2004, Vol. 5, p83
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Cross-species gene-expression comparison is a powerful tool for the discovery of evolutionarily conserved mechanisms and pathways of expression control. The usefulness of cDNA microarrays in this context is that broad areas of homology are compared and hybridization probes are sufficiently large that small inter-species differences in nucleotide sequence would not affect the analytical results. This comparative genomics approach would allow a common set of genes within a specific developmental, metabolic, or disease-related gene pathway to be evaluated in experimental models of human diseases. The objective of this study was to investigate the feasibility and reproducibility of cross-species analysis employing a human cDNA microarray as probe. Results: As a proof of principle, total RNA derived from human and bovine fetal brains was used as a source of labelled targets for hybridisation onto a human cDNA microarray composed of 349 characterised genes. Each gene was spotted 20 times representing 6,980 data points thus enabling highly reproducible spot quantification. Employing high stringency hybridisation and washing conditions, followed by data analysis, revealed slight differences in the expression levels and reproducibility of the signals between the two species. We also assigned each of the genes into three expression level categories- i.e. high, medium and low. The correlation co-efficient of cross hybridisation between the orthologous genes was 0.94. Verification of the array data by semiquantitative RT-PCR using common primer sequences enabled co-amplification of both human and bovine transcripts. Finally, we were able to assign gene names to previously uncharacterised bovine ESTs. Conclusions: Results of our study demonstrate the harnessing and utilisation power of comparative genomics and prove the feasibility of using human microarrays to facilitate the identification of co-expressed orthologous genes in common tissues derived from different species.
ACCESSION #
28859373

 

Related Articles

  • Technology: A wide (micro)array of options. Skipper, Magdalena // Nature Reviews Genetics;Feb2005, Vol. 6 Issue 2, p88 

    Discusses the use of microarrays on studies regarding gene expression, genotyping and in comparative genomic hybridization. Information on studies regarding genotyping experiments; Effects of the combination of gene expression and genotyping; Advantage of using the mRNA-based method.

  • Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. Mane, Shrinivasrao P.; Evans, Clive; Cooper, Kristal L.; Crasta, Oswald R.; Folkerts, Otto; Hutchison, Stephen K.; Harkins, Timothy T.; Thierry-Mieg, Danielle; Thierry-Mieg, Jean; Jensen, Roderick V. // BMC Genomics;2009, Vol. 10, p264 

    Background: Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the...

  • An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays. Gadgil, Mugdha; Wei Lian; Gadgil, Chetan; Vivek Kapur; Wei-Shou Hu // BMC Genomics;2005, Vol. 6, p66 

    Background: DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. To compare a large number of samples, the 'reference design' is widely used,...

  • MULTIFACTORIAL GENETICS: MAPPING AND ANALYSIS OF QUANTITATIVE TRAIT LOCI IN EXPERIMENTAL POPULATIONS. Doerge, Rebecca W. // Nature Reviews Genetics;Jan2002, Vol. 3 Issue 1, p43 

    Simple statistical methods for the study of quantitative trait loci (QTL), such as analysis of variance, have given way to methods that involve several markers and high-resolution genetic maps. As a result, the mapping community has been provided with statistical and computational tools that...

  • Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles. Kitchen, Robert R.; Sabine, Vicky S.; Sims, Andrew H.; Macaskill, E. Jane; Renshaw, Lorna; Thomas, Jeremy S.; van Hemert, Jano I.; Dixon, J. Michael; Bartlett, John M. S. // BMC Genomics;2010, Vol. 11, p134 

    Background: Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple...

  • Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis. Walters, Kathie-Anne; Joyce, Michael A.; Thompson, Jill C.; Proll, Sean; Wallace, James; Smith, Maria W.; Furlong, Jeff; Tyrrell, D. Lorne; Katze, Michael G. // Virology Journal;2006, Vol. 3, p37 

    Background: Many model systems of human viral disease involve human-mouse chimeric tissue. One such system is the recently developed SCID-beige/Alb-uPA mouse model of hepatitis C virus (HCV) infection which involves a human-mouse chimeric liver. The use of functional genomics to study HCV...

  • 5,000 RNAi experiments on a chip. Lehner, Ben; Fraser, Andrew G. // Nature Methods;Nov2004, Vol. 1 Issue 2, p103 

    The article highlights developments relevant to the use of microarrays, which has revolutionized gene expression studies and are expected to benefit studies on genome-wide RNA interference screens. Sabatini and colleagues have adapted their reverse-transfection technology to allow them to...

  • Increased DNA microarray hybridization specificity using sscDNA targets. Barker, Christopher S; Griffin, Chandi; Dolganov, Gregory M; Hanspers, Kristina; Hwa Yang, Jean Yee; Erle, David J // BMC Genomics;2005, Vol. 6, p57 

    Background: The most widely used amplification method for microarray analysis of gene expression uses T7 RNA polymerase-driven in vitro transcription (IVT) to produce complementary RNA (cRNA) that can be hybridized to arrays. However, multiple rounds of amplification are required when assaying...

  • Application of four dyes in gene expression analyses by microarrays. Staal, Yvonne CM; van Herwijnen, Marcel HM; van Schooten, Frederik J; van Delft, Joost HM // BMC Genomics;2005, Vol. 6, p101 

    Background: DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed simultaneously by applying four different fluorescent dyes. Results:...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics