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

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

“…Fluorescence recovery after photo bleaching (FRAP), single molecule, in vivo footprinting, and other in vivo measurements of DNA binding generally support these thermodynamic predictions: most indicate that >90% of transcription factors molecules contact DNA (13)(14)(15)(16)(17)(18), although estimates of only ∼25% have been proposed in some FRAP studies (19). The sequence-independent, electrostatic affinity that all transcription factors have for DNA (K d ∼10 −6 M) is sufficient to cause most molecules to be bound to DNA (10,12,15).…”

“…It has long been appreciated, however, that low-occupancy interactions that do not affect transcription in cis will affect the system in trans by lowering the concentration of unbound transcription factor molecules, which will in turn necessarily reduce the occupancy levels of transcription factors at highly bound, functional cis-regulatory regions (10)(11)(12)(13)(14)(15)(16)(17)(18). Low-occupancy DNA binding could in this sense be said to be functional, but it is a very different function from that of regulating nearby genes via cis-regulatory regions, and most low-occupancy interactions are not under strong natural selection in the same way that direct regulatory interactions in cis-regulatory regions are (Fig.…”

“…Multiple lines of evidence suggest that transcription factors in all organisms make extensive, low-occupancy, nonfunctional interactions that are thermodynamically driven by the concentrations of transcription factors and DNA in cells (10)(11)(12)(13)(14)(15)(16)(17)(18); reviewed in ref.…”

Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict

“…Accordingly, polymorphic Y chromosomes might exert their effects on gene regulation by serving as a differential sink for the binding of chromatin regulators or other DNA-binding proteins, which may lead to the titration of these proteins at other genomic locations (13). The feasibility of such satellite-repeat-sink model has been demonstrated in the case of the transcription factor C/EBP alpha, which binds to satellite repeat alpha in mice (32). Moreover, analyses of enhancer-trap mutants whose expression is modulated by the Y chromosome identified a multi-megabase segment in the Y chromosome that acts as a transregulator of a lacZ reporter expression (33).…”

PIASy Represses CCAAT/Enhancer-binding Protein δ (C/EBPδ) Transcriptional Activity by Sequestering C/EBPδ to the Nuclear Periphery

“…These collective findings highlight the complexity of the role of PIASy and sumoylation in the regulation of individual transcription factors. In addition, it has recently been reported that C/EBP␣ transcriptional activity may be regulated by sequestration in transcriptionally inactive pericentromeric heterochromatin (55). Since the PIASy SAP domain binds ATrich DNA present in scaffold attachment regions, also called matrix attachment regions, it is possible that subnuclear sequestration could include the binding of C/EBP␦ to AT-rich or repetitive DNA present at the nuclear periphery (31,56).…”