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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.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Hope CM,Rebay I,Reinitz J

doi

10.1016/j.bpj.2016.11.901

subject

Has Abstract

pub_date

2017-01-10 00:00:00

pages

180-192

issue

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(16)31931-2

journal_volume

112

pub_type

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DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan.