1) The time-dependent MMTV transcriptional response to liganded GR is complex, with a rapid initial activation phase followed by the irreversible repression of high transcription rates. We have characterized the global response to GR action in mouse cells, identifying 1100 responsive genes. The response of both positively and negatively regulated genes is surprising complex, with activation and repression profiles dramatically varying over time. The examination of nascent transcripts for a subset of these genes indicates at least six classes of gene response (63). 2) Using ChIP-Chip and ChIP-Seq methodologies, we characterized GR regulatory elements throughout the murine genome. While many GR binding sites are found in the immediate vicinity of target promoters, a large set of GR interaction sites are located at great distances from any promoter element. 3) We have characterized the chromatin landscape at local GR interaction events. We find that GR binding to regulatory elements invariably results in local chromatin transitions identified as DNaseI hypersensitive sites (DHSs). While GR can bind to unremodeled nucleosomes in vitro, we report that GR interaction with the chromatin fiber always leads to the local reorganization of nucleosomes, indicating the chromatin remodeling is a universal feature of GR template binding. 4) GR induced chromatin remodeling in model systems has been correlated with Swi/Snf action. While a subset of chromatin transitions induced by GR in vivo also require this remodeling system, we find that many nucleosome remodeling events are Swi/Snf independent. Furthermore, GR frequently interacts at sites already hypersensitive to DNaseI attack, and these sites can be either Swi/Snf dependent or independent. Thus GR can mobilize remodeling systems other than Swi/Snf, and can also interact at pre-existing sites of chromatin remodeling. There are four types of GR chromatin interactions, two GR-dependent or -independent groups each comprising subsets either requiring or independent of Swi-Snf action. 5) The local organization of the GR chromatin interaction sites is highly cell specific, and strongly correlated with GR transcriptional response. GR sites linked to promoters that are non-responsive in a given cell type are refractory to GR directed remodeling, and resistant to receptor binding. This leads to the hypothesis that local chromatin structural organization in a given cell type is a major determinant of tissue specific GR action. 6) Long range interactions between GR regulatory sites and target promoters have been discovered and characterized using the ACT modification of chromosome conformation capture (3C) methodology. These interactions suggest that GR binding elements can function partially through a large scale looping mechanism. 7) The potential directed movement of chromosomal loci within mammalian nuclei is an important, although controversial issue in current cell biology. We observed that a fluorescently tagged gene locus moves in real time to localize with cajal bodies in HeLa cells. Furthermore, suppression of actin expression through the use of dominant negative actin mutants suggests a role for this activity in the directed movement. These findings suggest force vectors are present that can direct the movement of specific chromosome elements.
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