Functional sequestration of transcription factor activity by repetitive DNA

Higher eukaryote genomes contain repetitive DNAs, often concentrated in transcriptionally inactive heterochromatin. Although repetitive DNAs are not typically considered as regulatory elements that directly affect transcription, they can contain binding sites for some transcription factors. Here, we demonstrate that binding of the transcription factor CCAAT/enhancer-binding protein alpha (C/EBP alpha) to the mouse major alpha-satellite repetitive DNA sequesters C/EBP alpha in the transcriptionally inert pericentromeric heterochromatin. We find that this sequestration reduces the transcriptional capacity of C/EBP alpha. Functional sequestration of C/EBP alpha was demonstrated by experimentally reducing C/EBP alpha binding to the major alpha-satellite DNA, which elevated the concentration of C/EBP alpha in the non-heterochromatic subcompartment of the cell nucleus. The reduction in C/EBP alpha binding to alpha-satellite DNA was induced by the co-expression of the transcription factor Pit-1, which removes C/EBP alpha from the heterochromatic compartment, and by the introduction of an altered-specificity mutation into C/EBP alpha that reduces binding to alpha-satellite DNA but permits normal binding to sites in some gene promoters. In both cases the loss of alpha-satellite DNA binding coincided with an elevation in the binding of C/EBP alpha to a promoter and an increased transcriptional output from that promoter. Thus, the binding of C/EBP alpha to this highly repetitive DNA reduced the amount of C/EBP alpha available for binding to and regulation of this promoter. The functional sequestration of some transcription factors through binding to repetitive DNAs may represent an underappreciated mechanism controlling transcription output.