Abstract
Nucleosomes can block access to transcription factors. Thus the precise localization of nucleosomes relative to transcription start sites and other factor binding sites is expected to be a critical component of transcriptional regulation. Recently developed microarray approaches have allowed the rapid mapping of nucleosome positions over hundreds of kilobases (kb) of human genomic DNA, although these approaches have not yet been widely used to measure chromatin changes associated with changes in transcription. Here, we use custom tiling microarrays to reveal changes in nucleosome positions and abundance that occur when hormone-bound glucocorticoid receptor (GR) binds to sites near target gene promoters in human osteosarcoma cells. The most striking change is an increase in measured nucleosome occupancy at sites spanning ∼1 kb upstream and downstream of transcription start sites, which occurs one hour after addition of hormone, but is lost at 4 hours. Unexpectedly, this increase was seen both on GR-regulated and GR-non-regulated genes. In addition, the human SWI/SNF chromatin remodeling factor (a GR co-activator) was found to be important for increased occupancy upon hormone treatment and also for low nucleosome occupancy without hormone. Most surprisingly, similar increases in nucleosome occupancy were also seen on both regulated and non-regulated promoters during differentiation of human myeloid leukemia cells and upon activation of human CD4+ T-cells. These results indicate that dramatic changes in chromatin structure over ∼2 kb of human promoters may occur genomewide and in response to a variety of stimuli, and suggest novel models for transcriptional regulation.
Highlights
Nucleosomes can inhibit transcription by blocking the access of transcription factors to their sites on DNA
The array covered several genes that are not regulated by glucocorticoid receptor (GR): including, CSF1 and CD44, CDK1, E2F1, CCNE1, CCNB2, CCNA1, and the housekeeping core metabolic gene GAPDH
At the outset of this study we hypothesized that the recruitment of hSWI/SNF to GR binding sites and GR-regulated promoters might result in discrete changes in nucleosome positions that would activate or repress transcription by allowing or blocking the binding of transcription factors to DNA
Summary
Nucleosomes can inhibit transcription by blocking the access of transcription factors to their sites on DNA. Elegans to man [5,6,7,10,12] This sequence-directed arrangement of nucleosomes is likely to directly impact transcription, since functional transcription factor binding sites (consensus sites that are evolutionarily conserved and/or known to be bound in vivo) were much more frequently found in linker regions than in DNA covered by nucleosomes, and since start sites of active genes were frequently devoid of nucleosomes [2,3,4,6,13]. These studies indicate that nucleosome positioning will be involved in transcriptional regulation much more often than was initially suspected, and emphasize the need for a deeper understanding of how nucleosome positions are functionally controlled
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