A Phase Separation Model for Transcriptional Control

Abstract

Phase-separated multi-molecular assemblies provide a general regulatory mechanism to compartmentalize biochemical reactions within cells. We propose that a phase separation model explains established and recently described features of transcriptional control. These features include the formation of super-enhancers, the sensitivity of super-enhancers to perturbation, the transcriptional bursting patterns of enhancers, and the ability of an enhancer to produce simultaneous activation at multiple genes. This model provides a conceptual framework to further explore principles of gene control in mammals.

Keywords: bursting; co-operativity; enhancer; gene control; nuclear body; phase separation; super-enhancer; transcription; transcriptional burst.

Figure 1. Models and features of super-enhancers and typical enhancers

A. Schematic depiction of the classic model of co-operativity exemplified for typical enhancers and super-enhancers. The higher density of transcriptional regulators (referred to as “activators”) through co-operative binding to DNA binding sites is thought to contribute to both higher transcriptional output and increased sensitivity to activator concentration at super-enhancers. Image adapted from (Loven et al., 2013). B. ChIP-seq binding profiles for RNA polymerase II (RNAPII) and the indicated transcriptional cofactors and chromatin regulators at the POLE4 and miR-290-295 loci in murine embryonic stem cells. The transcription factor binding profile is a merged ChIP-seq binding profile of the TFs Oct4, Sox2, and Nanog. rpm/bp, reads per million per base pair. Image adapted from (Hnisz et al., 2013). C. ChIA-PET interactions at the RUNX1 locus displayed above the ChIP-Seq profiles of H3K27Ac in human T-cells. The ChIA-PET interactions indicate frequent physical contact between the H3K27Ac occupied regions within the super-enhancer and the promoter of RUNX1.

Figure 2. A simple phase separation model of transcriptional control

A. Schematic representation of the biological system that can form the phase-separated multi-molecular complex of transcriptional regulators at a super-enhancer – gene locus. B. Simplified representation of the biological system, and parameters of the model that could lead to phase separation. “M” denotes modification of residues that are able to form cross-links when modified. C. Dependence of transcriptional activity (TA) on the valency parameter for super-enhancers (consisting of N=50 chains), and typical enhancers (consisting of N=10 chains). The proxy for transcriptional activity (TA) is defined as the size of the largest cluster of cross-linked chains, scaled by the total number of chains. The valency is scaled such that the actual valency is divided by a reference number of 3. The solid lines indicate the mean and the dashed lines indicate twice the standard deviation in 50 simulations. The value of K_eq and modifier/demodifier ratio was kept constant. HC= Hill coefficient, which is a classic metric to describe co-operative behavior. The inset shows the dependency of the Hill co-efficient on the number of chains, or components, in the system.

Figure 3. Super-enhancer vulnerability

A. Enhancer activities of the fragments of the IGLL5 super-enhancer (red) and the PDHX typical enhancer (gray) after treatment with the BRD4 inhibitor JQ1 at the indicated concentrations. Enhancer activity was measured in luciferase reporter assays in human multiple myeloma cells. Note that JQ1 inhibits ~50% of luciferase expression driven by the super-enhancer at a 10-fold lower concentration than luciferase expression driven by the typical enhancer (25nM vs 250nM). Data and image adapted from (Loven et al., 2013). B. Dependence of transcriptional activity (TA) on the demodifier/modifier ratio for super-enhancers (consisting of N=50 chains), and typical enhancers (consisting of N=10 chains). The proxy for transcriptional activity (TA) is defined as the size of the largest cluster of cross-linked chains, scaled by the total number of chains. The solid lines indicate the mean and the dashed lines indicate twice the standard deviation of 50 simulations. K_eq and f were kept constant. Note that increasing the demodifier levels is equivalent to inhibiting cross-linking (i.e. reducing valency). TA is normalized to the value at log (demodifier/modifier) = −1.5 and the ordinate shows the normalized TA on a log scale.

Figure 4. Transcriptional bursting

A. Representative traces of transcriptional activity in individual nuclei of Drosophila embryos. Transcriptional activity was measured by visualizing nascent RNAs using fluorescent probes. Top panel shows a representative trace produced by a weak enhancer, the bottom panel shows a representative trace produced by a strong enhancer. Data and image adapted from (Fukaya et al., 2016) B. Simulation of transcriptional activity (TA) of super-enhancers (N=50 chains), and typical enhancers (N=10 chains) over time recapitulates bursting behavior of weak and strong enhancers. C. Model of synchronous activation of two gene promoters by a shared enhancer.

Figure 5. Transcriptional control phase separation in vivo

Model of a phases-separated complex at gene regulatory elements. Some of the candidate transcriptional regulators forming complex are highlighted. P-CTD denotes the phosphorylated C-terminal domain of RNA polymerase II (RNAPII). Chemical modifications of nucleosomes (Acetylation: Ac; and Methylation: Me3) are also highlighted. Divergent transcription at enhancers and promoters produces nascent RNAs that can be bound by RNA splicing factors. Potential interactions between the components are displayed as dashed lines.