The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression. However, little is known about genomic features of associating loci and how they relate to rapid transcriptional regulation by an inducible transcription factor. We combined genome-wide interaction profiling with expression, protein occupancy, and chromatin accessibility profiles, to investigate the properties of genomic loci that are in close proximity. We find that the nucleus is non-randomly organized in a conformation that correlates with gene expression. These hubs are enriched for specific transcription factors binding sites, and DNaseI hypersensitive sites. These findings indicate that chromosomal segments containing specific regulatory elements and open chromatin are arranged in nuclear domains that are poised to respond to diverse signals in general, and permit efficient gene regulation.
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