Enhancer-Insulator Pairing Reveals Heterogeneous Dynamics in Long-Distance 3D Gene Regulation

Abstract

Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Short DNA sequences, known as enhancers (50–1500 base pairs), help coordinate these cascades by attracting regulatory proteins that enhance the transcription by binding to distal gene promoters. In humans, there are hundreds of thousands of enhancers dispersed across the genome, which poses a challenging coordination task to prevent unintended gene activation. To mitigate this problem, the genome contains insulator elements that block enhancer-promoter interactions. However, there is an open problem with how the insulation works, especially as enhancer-insulator pairs may be separated by millions of base pairs. Based on recent empirical data from Hi-C experiments, this paper proposes a new mechanism that challenges the common paradigm that rests on specific insulator-insulator interactions. Instead, this paper introduces a stochastic looping model where insulators bind weakly to chromatin rather than other insulators. After calibrating the model to experimental data, we use simulations to study the broad distribution of hitting times between an enhancer and a promoter when insulators are present. We find parameter regimes with large differences between average and most probable hitting times. This makes it difficult to assign a typical timescale and hints at highly defocused regulation times. We also map our computational model onto a resetting problem that allows us to derive several analytical results. Besides offering new insights into enhancer-insulator interactions, our paper advances the understanding of gene regulatory networks and causal connections between genome folding and gene activation. Published by the American Physical Society 2024