1) Using ChIP-Chip and ChIP-Seq methodologies, we characterized transcription factor regulatory elements throughout the murine and human genomes. While many transcription factor binding sites are found in the immediate vicinity of target promoters, a large set of transcription factor interaction sites are located at great distances from any promoter element. 2) We have characterized the chromatin landscape at local transcription factor interaction events. We find that transcription factor binding to regulatory elements usually results in local chromatin transitions identified as DNaseI hypersensitive sites (DHSs). While transcription factors can bind to unremodeled nucleosomes in vitro, we report that transcription factor interactions with the chromatin fiber always leads to the local reorganization of nucleosomes, indicating the chromatin remodeling is a universal feature of transcription factor template binding. 3) Transcription factor induced chromatin remodeling in model systems has been correlated with ATP-dependent chromatin remodeler action. Transcription factors frequently interact at sites already hypersensitive to DNaseI attack. Thus transcription factors can mobilize remodeling systems and interact either at pre-existing sites of chromatin remodeling or newly created sites. There are four types of transcription factor chromatin interactions: factor-dependent sites are called de novo events;factor-independent events are designated pre-programmed sites and reliy on other factors;each of these groups in turn comprise subsets requiring the action of different remodeling proteins. 4) The local organization of the factor chromatin interaction sites is highly cell specific, and strongly correlated with the transcriptional response. Factor sites linked to promoters that are non-responsive in a given cell type are refractory to factor directed remodeling, and resistant to factor binding. This leads to the hypothesis that local chromatin structural organization in a given cell type is a major determinant of tissue specific factor action. 5) Integration of these concepts led to the development of a new paradigm for transcription factor interaction with chromatin, termed """"""""assisted loading."""""""" 6) We are developing methods to utilize the DHS technology to characterize patient turmor status in terms of progression, metastatic potential, and response to therapy (Cancer Chromatin Profiling).
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