SUMMARY/ABSTRACT
Mechanisms of enhancer dynamics and assembly in gene regulation
Effective gene regulation is essential for the proper functioning of cells. Dynamic control of enhancer
repertoires drives stage-specific transcription during tissue development and disease progression. The overall
objective of our research program is to gain a fundamental understanding of the regulations of enhancer
dynamics in response to signaling and their effects on gene regulation, leading to innovative approaches to the
prevention and treatment of enhancer-related diseases. We propose the following two themes to pursue this
objective from multiple levels: from the enhancer chromatin organization, to the coordination of enhanceosome
components, and the molecular interactions that drive enhancer assembly. Supported by the NIGMS R01 grant
(R01GM137009) and other grants, we have made significant progress in both themes, and the results gained
from our previous studies form the strong foundation of this MIRA research program.
Theme 1: To profile the context-specific enhancer dynamics and understand its functional
significance. Our previous studies have revealed that enhancer dynamics can be induced by 1) acute
hormone stimulations, which can build up the active enhancer machinery in just minutes at many chromatin
sites to turn on gene expression, and 2) chronic disease progression towards tamoxifen resistance, which
reprograms the ERa cistrome to evade endocrine therapies in breast cancer. With these two established
model systems (acute and chronic signaling), we will 1) capture the dynamic enhancer chromatin organization
with multi-omics analyses and identify candidate key transcription factors associated with enhancer
reprogramming using bioinformatic approaches; 2) define stage-specific enhanceosome components using in
vivo proximity-dependent biotin labeling BioID/TurboID technologies; and 3) introduce a series of perturbations
to understand how disruption of enhancer dynamics affects transcriptional activation and cell state.
Theme 2: To decipher inter- and intra-molecular interactions of enhancer components and their
contributions to enhancer assembly. Enhancer activation relies on proper enhancer assembly, but the
molecular mechanisms of enhancer assembly (how protein-DNA and protein-protein interactions occur) are
unclear. We have revealed important principles of enhancer assembly, including combinatorial interactions of
multiple transcription factors on hormone-regulated enhancers, and phase-separated condensation mediated
by hormone receptor multivalent interactions. Further studies will employ a diverse set of genetic and genomic
approaches, as well as our recently established imaging-based approaches, including the LacO arrays/LacI-
fluorescence proteins system and a single-molecular tracking (SMT) imaging system. Specifically, we plan to
1) investigate the behaviors of homotypic and heterotypic multivalent interactions of enhanceosome
components and their contributions to enhancer assembly; and 2) dissect the intra-molecular interactions of
hormone receptors in response to ligand binding and their roles in regulating enhancer assembly and activity.