Signaling decoded in ENhanCEr states – a molecular basis for plasticity in development and differentiation

Introduction

Transcription is regulated by transcription factors (TFs) bound at enhancer elements located long distances from the genes they regulate. How does this account for dynamic responses to the environment via signaling? Canonical views invoke signal-induced changes in TF expression/modification or cofactor localization. However, here we suggest that TF occupancy could be present before and after the signal, establishing competence, ensuring plasticity, and blocking premature commitment.

ERK Signaling and Enhancer Regulation

For ERK signaling, a central regulator of embryonic stem cell (ESC) differentiation, we found that enhancers were regulated via selective recruitment of RNA Polymerase II (RNAPII) and associated cofactors. In this case, TFs do not play a direct role in enhancer regulation but safeguard future activation in response to changes in signaling.

Developmental Biology Implications

In the context of developmental biology, this paradigm could explain the dynamic nature of cell specification in the early mammalian embryo. In this proposal, we seek to understand enhancer-specific regulation by ERK and exploit our ability to manipulate ERK to disentangle mechanisms. We will focus on preimplantation development to explore how these phenomena explain plasticity.

Methodology

To circumvent heterogeneity created by feedback inhibition, we developed a unique ESC line for cell intrinsic and synchronous ERK induction. We combine these ESCs with rapid TF degradation mutants to isolate homogeneous cell states that can be exploited to generate unique datasets and identify key factors within the ERK response.

Research Focus

We address the following key areas:

1. How coactivator phosphorylation promotes selective recruitment of Mediator/RNAPII.
2. The fundamental nature of enhancer activity.
3. How uncoupling of transcriptional regulation from TF binding underpins developmental plasticity.

By exploiting our capacity to modulate enhancer activity via signaling, we not only address how signaling regulates transcription to drive differentiation choices but also how enhancers themselves regulate gene expression.