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Nucleic Acids Research 2005 33(20):6469-6485; doi:10.1093/nar/gki953
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Published online 14 November 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination

Takao Kasuga1, Jeffrey P. Townsend1,2, Chaoguang Tian1, Luz B. Gilbert1, Gertrud Mannhaupt3, John W. Taylor1 and N. Louise Glass1,*

1Department of Plant and Microbial Biology, University of California Berkeley, CA 94720-3102, USA 2Department of Molecular and Cell Biology, University of Connecticut Storrs, CT 06269, USA 3Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health D-85764 Neuherberg, Germany

*To whom correspondence should be addressed. Tel: +1 510 643 2399; Fax: +1 510 642 4995; Email: Lglass{at}nature.berkeley.edu

Received June 24, 2005. Revised September 22, 2005. Accepted October 19, 2005.

To test the inferences of spotted microarray technology against a biochemically well-studied process, we performed transcriptional profiling of conidial germination in the filamentous fungus, Neurospora crassa. We first constructed a 70 base oligomer microarray that assays 3366 predicted genes. To estimate the relative gene expression levels and changes in gene expression during conidial germination, we analyzed a circuit design of competitive hybridizations throughout a time course using a Bayesian analysis of gene expression level. Remarkable consistency of mRNA profiles with previously published northern data was observed. Genes were hierarchically clustered into groups with respect to their expression profiles over the time course of conidial germination. A functional classification database was employed to characterize the global picture of gene expression. Consensus motif searches identified a putative regulatory component associated with genes involved in ribosomal biogenesis. Our transcriptional profiling data correlate well with biochemical and physiological processes associated with conidial germination and will facilitate functional predictions of novel genes in N.crassa and other filamentous ascomycete species. Furthermore, our dataset on conidial germination allowed comparisons to transcriptional mechanisms associated with germination processes of diverse propagules, such as teliospores of the phytopathogenic fungus Ustilago maydis and spores of the social amoeba Dictyostelium discoideum.


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