| We used cDNA microarrays to systematically study the gene expression responses of HeLa cells and primary human lung fibroblasts to heat shock, endoplasmic reticulum stress, oxidative stress, crowding and, separately, UV irradiation. We developed computational tools and methods to efficiently integrate and analyze this and other large datasets. Hierarchical clustering of the combined data revealed groups of genes with coherent biological themes, including some that responded to specific stresses and others that responded to multiple types of stress. Fewer genes were induced by multiple stresses than in free-living yeasts, which have a large general stress response program, and most genes that were broadly induced are involved in cell-cell communication and other processes specific to higher organisms. We found substantial differences in the stress responses of the two cell types. For example, many genes were induced by oxidative/reductive stress in fibroblasts but not HeLa cells, while a group of transcription factors, including c-fos and c-jun, were induced by heat shock in HeLa cells but not in fibroblasts. The dataset is freely available for search and download at http://microarray-pubs.stanford.edu/human_stress/. We further characterized the role of the transcription factor HSF1 in the induction of the specific heat shock response. Previous work has implicated HSF1 as the primary, and possibly the only, transcription factor responsible for the transcriptional response to heat stress in mammalian cells. We characterized the heat shock response of mammalian cells by measuring changes in transcript levels and assaying binding of HSF1 to promoter regions for candidate heat shock genes. We found, as expected, that many heat shock-inducible genes have HSF1 binding sites (HSE) in their promoters that are bound by HSF1. Surprisingly, we detected no HSF1 binding for several heat-inducible genes. We detected HSF1 binding at only a fraction of HSE-containing promoters. Also, we found 48 genes with HSEs in their promoters that are bound by HSF1 but which nevertheless were not induced by heat shock. We verified the existence of HSF1-independent heat shock-induced genes in HSF1 knockout mouse fibroblasts; thus there must be another mechanism besides HSF1 that regulates the heat shock response. |
