News and Publications

Parallel Functional Genomics of Microbes

E. Winzeler, G. Oshiro,* D. Liang*

* Genomics Institute of the Novartis Research Foundation, San Diego, CA

Although the genome-sequencing projects produced gigabases of sequence information during the past 5 years, the precise cellular role of much of the sequences remains obscure. We are interested in discovering what these sequences do for cells. By examining the genome as a whole, we hope to make new observations that would not have been possible if only a single example of a cellular entity were studied. We have used the yeast Saccharomyces cerevisiae as a model system, but as their sequences become available, we are beginning to investigate the genomes of organisms with medical relevance. To this end we are functionally characterizing the genome of the malaria parasite Plasmodium falciparum. The ultimate goal of this research is to use genomic data to develop novel therapies for infectious diseases.

NEW IDENTIFICATION OF OPEN READING FRAMES

The identification of very small genes in a primary genome sequence is difficult. Using oligonucleotide arrays to examine the transcript levels of many of the unannotated open reading frames in the yeast genome, we identified several hundred small genes that are expressed at significant levels.

DNA REPLICATION

It is estimated that the yeast genome has about 400 origins of DNA replication, only a handful of which have been studied in detail. These origins fire at different times in the cell cycle and with different efficiencies. Using high-density arrays and a modification of the Meselson-Stahl density shift experiment, we characterized the timing of replication of the entire yeast genome and identified most of the efficient origins of DNA replication. We found that origins are associated with transposable elements and that the timing of replication is heterogeneous. Our goal is to use this information to determine exactly what constitutes an origin of replication at the molecular level.

GENETIC DIVERSITY

A major area of investigation in the postgenome era will be genetic diversity. We are developing methods to identify and analyze allelic variation in microorganisms (Fig. 1). We are using this technique to determine how different isolates of P falciparum differ from one another.

PARALLEL PHENOTYPIC ANALYSIS

Although analysis of transcription provides clues to the function of a gene, the phenotype of an organism that has a mutation in the gene is equally informative. We are using a mutant collection of 6200 different yeast strains, each of which carries a deletion in one of the estimated 6200 yeast genes. This collection can be screened to determine which genes play essential roles in many cellular processes.

PUBLICATIONS
Lockhart, D.J., Winzeler, E.A. Genomics, gene expression, and DNA arrays. Nature 405:827, 2000.

Primig, M., Williams, R.M., Winzeler, E.A., Tevzadze, G.G., Conway, A.R., Hwang, S.Y., Davis, R.W., Esposito, R.E. The core meiotic transcriptome in budding. Nat. Genet. 26:415, 2000.

Winzeler, E.A., Liang, H., Shoemaker, D.D., Davis, R.W. Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization. Novartis Found. Symp. 229:105, 2000.