NIH grant: Live-cell super-resolution imaging of enhancer-mediated gene bursting (1R35GM166242-01)

retained text

NIH grant 1R35GM166242-01: Live-cell super-resolution imaging of enhancer-mediated gene bursting
Institute: {'code': 'GM', 'abbreviation': 'NIGMS', 'name': 'National Institute of General Medical Sciences', 'admin_org_id': '12500024', 'admin_funding_url': ''}. PI: Manyu  Du. Award: $419939.
Start: 2026-08-01T00:00:00.
Abstract
The overall theme of my research program is to understand how enhancers and transcription machineries
organize in the 3D genome to regulate the target gene expression. We plan to address this problem from two
aspects: 1) at the single-cell level, we will characterize the function and dynamics of transcriptional
condensates in mouse embryonic stem cells and investigate the specificity of the condensate, the formation
and dissolution mechanisms, and their activity regulated by genome architecture; 2) at the developmental
level, we will study the mechanism of how transcriptional condensates achieve differential regulation of target
genes during development using the beta-globin regulation in mouse erythroleukemia cells as a model. In the
past years, we have made significant contributions in the first direction, and we excited to extend our research
to a new direction. New methods were developed and insights generated from these studies form the
foundation of this proposal. Theme1: In eukaryotes, RNA Pol II, Mediator and transcription activators form
transcription-dependent condensates in live mouse embryonic stem cells and enhance super-enhancer
controlled gene bursting in a proximity-dependent manner. However, molecular mechanisms of how
condensates function on gene bursting within the 3D genome is not fully resolved. The long-term goal of this
theme is to characterize the condensate specificity, to investigate their mechanisms of formation and regulation
by enhancers/enhancer RNAs, and to develop a full mechanistic understanding of how they interact with their
target regulatory elements. In the next five years, we plan to 1) test whether transcriptional condensate can
co-activate a reporter gene with different promoter specificity; 2) develop a labeling strategy to image and
study the roles of enhancer RNAs in condensate function; 3) selectively manipulate chromosomal interactions
and test how condensate-gene interactions and gene bursting change. Theme 2: The dynamics and functions
of transcriptional condensate have not been explored extensively due to their close-to-diffraction-limit size. The
long-term goal of this theme is to characterize the composition, dynamics and functions of transcriptional
condensates and their effect on beta-globin gene switching during erythroid differentiation, aiming to test the
function of condensates across different systems. In the next five years, we plan to: 1) test whether and how
transcriptional condensate dynamically controls beta-globin gene bursting; 2) develop a method to probe the
condensate composition and its changes during erythroid differentiation. We envision that our study will
provide significant insights and open new research directions on gene regulation.

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