A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus

The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis...

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Bibliographic Details
Published in:Nucleic acids research 2006-01, Vol.34 (1), p.185-200
Main Authors: Sartor, Maureen A., Zorn, Aaron M., Schwanekamp, Jennifer A., Halbleib, Danielle, Karyala, Saikumar, Howell, Michael L., Dean, Gary E., Medvedovic, Mario, Tomlinson, Craig R.
Format: Article
Language:English
Subjects:
Animals
Cells, Cultured
Gene Expression Profiling - methods
Gene Expression Regulation, Developmental
Genetic Variation
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide Probes
RNA, Messenger - chemistry
RNA, Messenger - metabolism
Species Specificity
Xenopus - embryology
Xenopus - genetics
Xenopus - metabolism
Xenopus laevis
Xenopus laevis - embryology
Xenopus laevis - genetics
Xenopus laevis - metabolism
Xenopus tropicalis
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Summary:The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis model system and the increasingly used X.tropicalis model system and assessed whether an X.tropicalis microarray platform can be used for X.laevis. These closely related species were also used to investigate a more general question: is there an association between mRNA sequence divergence and differences in gene expression levels? We carried out a comprehensive comparison of global gene expression profiles using microarrays of different tissues and developmental stages of X.laevis and X.tropicalis. We (i) show that the X.tropicalis probes provide an efficacious microarray platform for X.laevis, (ii) describe methods to compare interspecies mRNA profiles that correct differences in hybridization efficiency and (iii) show independently of hybridization bias that as mRNA sequence divergence increases between X.laevis and X.tropicalis differences in mRNA expression levels also increase.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkj413