Microarray Research in the Glass Lab
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People working on microarrays:
Takao Kasuga (postdoc)
Chaoguang Tian (postdoc)
Sarah Brown (graduate student, Glass Lab)
Luz B. Gilbert (graduate student, Taylor Lab)
Microarray Research in the Glass Lab
People working on microarrays:
Takao Kasuga (postdoc)
Chaoguang Tian (postdoc)
Sarah Brown (graduate student, Glass Lab)
Luz B. Gilbert (graduate student, Taylor Lab)
Research:
Neurospora crassa is characterized by a complex lifecycle; there are at least 28 distinct cell types. The DNA sequence of the 40 Mb genome of N. crassa encodes c.a. 10,000 genes. Functional annotation of these genes has succeeded largely on the basis of computer predictions using patterns recognized in characterized genes and homology searches to proteins in public protein databases. However, over 40% of the N. crassa genes have no counterpart in public databases and are listed as “hypothetical”. In an effort to elucidate transcriptional regulatory pathways in N. crassa as a model for filamentous fungi, we have been developing oligomer microarrays for transcriptional profiling experiments. Transcriptional profiling data has been used to predict biological function of novel genes in S. cerevisiae. Therefore, gene expression data generated by microarray technology can be used to expedite the annotation process of the N. crassa genome.
We designed a 70-mer oligonucleotide for each of the predicted genes in the N. crassa genome by using an oligonucleotide design program, ArrayOligoSelector. The ~10,500 oligonucleotides are spotted onto GAP microarray slides. Full genome N. crassa microarrays are available from the Fungal Genetics Stock Center.
We evaluated the performance of long oligomer arrays for transcriptional profiling by assessing gene expression patterns during asexual spore (conidial) germination; biochemical processes associated with conidial germination have been well characterized in N. crassa (1).
To estimate relative gene expression levels and changes in gene expression during conidial germination, we analyzed a circuit design of competitive hybridizations throughout germination using a Bayesian Analysis of Gene Expression Level (BAGEL) (2-4).
Genes were hierarchically clustered into groups with respect to their expression profiles over the time course of conidial germination. The Functional Catalogue (FunCat) was employed to formulate a global picture of gene expression during conidial germination in N. crassa.
Genes that showed differential expression during conidial germination, and which also had annotation were classified according to functional categories (FunCat). This analysis showed co-regulation of genes associated with biochemical processes that occur during conidial germination.
Our dataset on conidial germination will allow comparisons to transcriptional mechanisms associated with germination of diverse propagule, such as spores in protist species, seed and pollen germination and plants and sexual spore germination in fungi. The conidial germination transcriptional profiling data is available at the Neurospora crassa Functional Genomics Database
PUBLICATIONS
Tian, C., T. Kasuga, M. S. Sachs and N. L. Glass, 2007. Transcriptional profiling of cross pathway control in Neurospora crassa: Comparative analysis of the Gcn4 and CPC1 regulons Eukaryot Cell 6:1018-29. Click here for abstract
Dunlap, J.C. , Borkovich, K.A., Henn, M.R., Turner, G.E., Sachs, M.S., Glass, N.L., McClusky, K., Plamann, M., Galagan, J.E., Birren, B.W., Weiss, R.L., Townsend, J.P., Nelson, M.A., Lambreghts. R., Colot, H.V., Park, G., Collopy, P., Ringelberg, C., Crew, C., Litvinkova, L.,DeCaprio, D. Hood, H.M., Crawford, M., Koerhsen, M., Montgomery, P., Larson, L., Pearson, M., Kasuga, T., Tian, C., Batürkmen, M. and Xu, J. Enabling a community to dissect an organism: Overview of The Neurospora Functional Genomics Project. 2007. Adv. Genetics 57:49-96. Click here for abstract
Kasuga, T., J. P. Townsend, C. Tian, L. B. Gilbert, G. Mannhaupt, J. W. Taylor and N. L. Glass (2005)
Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Res. 33:6469-85.
Click here for abstract
Meiklejohn, C.D. and J.P. Townsend, 2005. A Bayesian method for analysing spotted microarray data. Briefings in Bioinformatics 6(4): 318-330.
Townsend, J.P. 2004. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 5: 54.
Townsend, J.P., and D.L. Hartl. 2002. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 3 (12): research0071.1-0071.16.
Useful links:
-Broad Institute Neurospora crassa release 7