Environmental stress causes changes in an organism's gene expression, caused mainly by the activity of transcription factors. In higher eukaryotes, transcription factors acting through their binding sites can be potent activators or repressors even when they are located thousands of base-pairs away from the transcriptional start site. The identification of new cis-regulatory sequences is possible by examining regions near genes with similar expression profiles for common motifs. Once identified, these cis-regulatory motifs can be tested for activity. In this project mammalian microarray experiments from other researchers will be used to cluster genes, and novel motifs discovered through computational approaches developed in this proposal will be given back to those labs for further experimental testing. The upstream regions of each of the genes with a significant change in mRNA expression will be compared with the available upstream region of all of the genes in the microarray experiment to isolate motifs more prevalent in the differentially expressed genes. Some of the tools developed in the Church lab for motif finding in yeast will be applied to mammalian motifs, including AlignACE. Another goal is to use the database of all the upstream regions to develop more sensitive algorithms for finding novel motifs. In addition to clustering based on a single condition, genes will be clustered based on their change in expression over time. The sequence in cis to the genes in these time-course experiments will then be searched for novel enhancers. Novel motifs in mammalian systems will be an invaluable resource in future studies involving gene characterization, including identification of gene pathways and networks. ? ?
