The availability of the complete nucleotide sequence of the genomes of several organisms, including the human, presents us with an unprecedented opportunity and challenge. How can we use this wealth of information to better understand the biology of organisms in molecular detail? The use of microarrays (chips) provides a powerful experimental approach for exploring the molecular biology of organisms on a genome-wide scale. Research in our lab is centered around the use of microarrays as an experimental tool for analyzing transcriptional programs and mechanisms in eukaryotic cells.

There are two main areas of interest.

i) Use of yeast as a model system to map the genome-wide physical interactions of transcription factors with their chromosomal targets. We have recently designed and made DNA microarrays that include not only the coding region of every yeast gene, but also every yeast promoter. We are combining chromatin immunoprecipitation and hybridization to promoter microarrays to map the genome-wide, in vivo DNA binding distribution of a variety of transcription factors. In conjunction with this, transcriptional targets are identified by analyzing global changes in gene expression in response to modulation of the given factor. We can thus, for the first time, obtain a richly detailed, dynamic picture of a eukaryotic genome, both in terms of its physical representation inside the cell as well its transcriptional behaviour in response to various regulatory inputs. This effort with yeast will also lay the groundwork for application of this approach to mapping the interactions of transcriptional regulators with higher eukaryotic promoters.

ii) A systematic and comprehensive analysis of transcriptional control mechanisms in cellular proliferation and cancer biology. The expression of several transcription factors is altered during the transition of human cells from quiescence to proliferation. Disruption of the normal function of such transcription factors underlies many pathological states, including cancer. We are using human cDNA microarrays containing tens of thousands of human genes to determine the downstream targets of oncogenic transcription factors. This is done by expressing the regulators under the control of inducible promoters and using dominant negative alleles and chemical inhibitors, in cell lines and under conditions when the transcription factors are known to be active. Determining the targets of oncogenic transcription factors is likely to enhance our understanding of the role of these oncogenes in normal cell proliferation and in cancer.

Concurrently, we are developing other novel approaches to genome-scale biology involving microarrays, improving the technology, as well as developing the analytical or computational tools required for fully exploiting the power of this approach.