title: DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan.
abstract: Transcription factors use both protein-DNA and protein-protein interactions to assemble appropriate complexes to regulate gene expression. Although most transcription factors operate as monomers or dimers, a few, including the E26 transformation-specific family repressors Drosophila melanogaster Yan and its human homolog TEL/ETV6, can polymerize. Although polymerization is required for both the normal and oncogenic function of Yan and TEL/ETV6, the mechanisms by which it influences the recruitment, organization, and stability of transcriptional complexes remain poorly understood. Further, a quantitative description of the DNA occupancy of a polymerizing transcription factor is lacking, and such a description would have broader applications to the conceptually related area of polymerizing chromatin regulators. To expand the theoretical basis for understanding how the oligomeric state of a transcriptional regulator influences its chromatin occupancy and function, we leveraged the extensive biochemical characterization of E26 transformation-specific factors to develop a mathematical model of Yan occupancy at chemical equilibrium. We find that spreading condensation from a specific binding site can take place in a path-independent manner given reasonable values of the free energies of specific and non-specific DNA binding and protein-protein cooperativity. Our calculations show that polymerization confers upon a transcription factor the unique ability to extend occupancy across DNA regions far from specific binding sites. In contrast, dimerization promotes recruitment to clustered binding sites and maximizes discrimination between specific and non-specific sites. We speculate that the association with non-specific DNA afforded by polymerization may enable regulatory behaviors that are well-suited to transcriptional repressors but perhaps incompatible with precise activation.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, The University of Chicago, Chicago, Illinois.
authors.forename: C Matthew
authors.initials: CM
authors.lastname: Hope
authors.affiliation: Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois; Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois. Electronic address: irebay@uchicago.edu.
authors.forename: Ilaria
authors.initials: I
authors.lastname: Rebay
authors.affiliation: Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois; Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois; Department of Statistics, The University of Chicago, Chicago, Illinois. Electronic address: reinitz@galton.uchicago.edu.
authors.forename: John
authors.initials: J
authors.lastname: Reinitz
mesh_terms: D000818:Animals; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D029721:Drosophila Proteins / Q000737:chemistry* / Q000378:metabolism*; D005136:Eye Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: C076188:AOP protein, Drosophila; D029721:Drosophila Proteins; D005136:Eye Proteins; D012097:Repressor Proteins; D004247:DNA