A central question in eukaryotic gene expression is how the activation of gene expression
depends simultaneously on transcription factor availability and quantitative features of the
chromatin environment at different genomic locations (Fig. 1A). 1 Eukaryotic transcription
factors commonly regulate multiple genes, yet extracellular stimuli that activate transcription
factors result in selective expression of only a subset of these genes. The sequence and
arrangement of transcription factor binding sites in different promoters cannot fully explain …

Higher order chromatin structure in eukaryotes can lead to differential gene expression in
response to the same transcription factor; however, how transcription factor inputs integrate
with quantitative features of the chromatin environment to regulate gene expression is not
clear. In vitro models of HIV gene regulation, in which repressive mechanisms acting locally
at an integration site keep proviruses transcriptionally silent until appropriately stimulated,
provide a powerful system to study gene expression regulation in different chromatin …