Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression

Abstract

The organization of binding sites in cis-regulatory elements (CREs) can influence gene expression through a combination of physical mechanisms, ranging from direct interactions between TF molecules to DNA looping and transient chromatin interactions. The study of simple and common building blocks in promoters and other CREs allows us to dissect how all of these mechanisms work together. Many adjacent TF binding sites for the same TF species form homotypic clusters, and these CRE architecture building blocks serve as a prime candidate for understanding interacting transcriptional mechanisms. Homotypic clusters are prevalent in both bacterial and eukaryotic genomes, and are present in both promoters as well as more distal enhancer/silencer elements. Here, we review previous theoretical and experimental studies that show how the complexity (number of binding sites) and spatial organization (distance between sites and overall distance from transcription start sites) of homotypic clusters influence gene expression. In particular, we describe how homotypic clusters modulate the temporal dynamics of TF binding, a mechanism that can affect gene expression, but which has not yet been sufficiently characterized. We propose further experiments on homotypic clusters that would be useful in developing mechanistic models of gene expression.

Keywords: Cooperativity; Enhancers; Facilitated diffusion; Massively parallel gene expression assays; Mechanistic models.

Fig. 1

Binding configurations in a homotypic cluster of two binding sites. To the right, we present the level of gene expression, given various different mechanisms of TF action. The mechanisms of TF action we include is AND logic (all the TFs must be bound for transcription to occur), OR logic (at least one TF must be bound for transcription to occur), independent symmetric (each TF independently contributes to gene expression), independent asymmetric (each TF independently contributes to gene expression, but the effect on transcription is also dependent on the position of the binding site) and cooperative (there may be some leaky expression when each TF independently binds, but there are synergistic effects when both TFs are bound).

Fig. 2

Cooperative binding assuming direct TF–TF interactions. We illustrate the cases of TF binding independently to their binding sites (A) and cooperatively through direct TF–TF interactions (B). (A) We assumed that the binding of TF molecules to the binding sites is independent and in this case the proportion of bound sites increases gradually with the TF concentration. (B) We assumed that direct TF–TF interaction can stabilize the binding and, in this scenario, the proportion of bound sites as a function of TF concentration displays a sigmoid shape. Note that on the right side we plot the proportion of sites bound in each case as a function of TF concentration.

Fig. 3

The influence of homotypic clusters on facilitated diffusion. (A) We illustrate the process of facilitated diffusion for a single binding site: a TF can find the binding site by 3D diffusion or 1D diffusion from either side (orange arrows). If a TF randomly binds within the sliding window (illustrated by the red bar) then it will diffuse to the binding site with high probability. Therefore, the longer the red bar, the higher the probability a TF will find its binding site. In panels (B–D), we illustrate three ways in which homotypic clusters influence TF search time and occupancy within a facilitated diffusion context. (B) The sliding window is expanded by the presence of the homotypic clusters, so it is faster to find a site in a cluster than an individual site. (C) Once a TF is bound, it may slide or hop randomly to the neighboring binding site, thereby enhancing TF occupancy. (D) If one TF is already bound to a binding site, then it restricts the sliding length by which a second TF can find its binding site, which we refer to as the barrier effect. Therefore, homotypic clusters influence temporal dynamics of TF binding in a variety of ways.