Quantification and potential functional relevanceof binding cooperativity of adjacent transcriptionfactors on DNA

Abstract

In eukaryotes, expression of a particular gene is regulated by a combination of transcription factors (TFs) bound on regulatory regions of the genomic DNA (promoters and enhancers). Recent advances in genomic sequencing technology have allowed measurements of TFs footprints and binding affinities on DNA at the single-molecule level, permitting the probing of binding cooperativity among adjacent TFs. This necessitates quantitative descriptions of TFs binding cooperativity and understanding of its potential functional relevance. In this study, we show that, thermodynamically, the binding affinities of two adjacent TFs can either increase together (positive cooperativity) or decrease together (negative cooperativity), rather than changing in opposite directions. Their binding cooperativity can be quantified by the{gamma} coefficient, which is independent of TF concentrations, and can be determined by single-molecule binding reads either from in vitro thermodynamic condition or cellular condition of non-equilibrium steady state (NESS). The functional relevance of positive cooperativity, which has been extensively discussed in the literature, is the sigmoidal binding curve around a TF concentration threshold (analogous to oxygen binding to hemoglobin), whereas the functional relevance of negative cooperativity is two-fold. First, mutual exclusion of the two TFs enables bidirectional gene switching similar to CI-Cro system in phage{lambda} . Second, under a non-equilibrium steady-state condition, in which TFs often exhibit intranuclear concentration fluctuations, negative binding cooperativity assures fast TF dissociation from DNA and hence rapid response for gene expression regulation. Significance StatementIn eukaryotes, multiple transcription factors (TFs) bind to regulatory regions of DNA to control gene expression. The binding affinity of one TF to a specific DNA site is influenced by the binding of another TF at an adjacent site, exhibiting either positive or negative cooperativity (the TFs either strengthen or weaken each others binding). Here we present metric for such cooperativity from experimental measurables. Functionally, positive cooperativity assures sensitive response above a threshold of TF concentrations, whereas functional roles for negative cooperativity might be two folds: First, mutual exclusion of TFs binding enables bidirectional gene switching. Second, as TF concentrations oscillate under non-equilibrium steady-state condition, negative binding cooperativity assures fast TF dissociation, hence rapid switching of transcription.