Functional Sequestration of Transcription Factor Activity by Repetitive DNA*

Abstract

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 α (C/EBPα) to the mouse major α-satellite repetitive DNA sequesters C/EBPα in the transcriptionally inert pericentromeric heterochromatin. We find that this sequestration reduces the transcriptional capacity of C/EBPα. Functional sequestration of C/EBPα was demonstrated by experimentally reducing C/EBPα binding to the major α-satellite DNA, which elevated the concentration of C/EBPα in the non-heterochromatic subcompartment of the cell nucleus. The reduction in C/EBPα binding to α-satellite DNA was induced by the co-expression of the transcription factor Pit-1, which removes C/EBPα from the heterochromatic compartment, and by the introduction of an altered-specificity mutation into C/EBPα that reduces binding to α-satellite DNA but permits normal binding to sites in some gene promoters. In both cases the loss of α-satellite DNA binding coincided with an elevation in the binding of C/EBPα to a promoter and an increased transcriptional output from that promoter. Thus, the binding of C/EBPα to this highly repetitive DNA reduced the amount of C/EBPα 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.