(12b) Enhancer-Mediated Regulation of Transcriptional Bursting

My research interests lie in quantitative analysis of regulation in development, using both experimental and computational approaches. I completed my Ph.D. studies with Professor Stanislav Shvartsman in the department of Chemical and Biological engineering at Princeton University. Using a combination of genetic tools, high-throughput imaging, and mathematical modeling, I reconstructed developmental dynamics of the highly conserved ERK enzymatic activity from snapshots of fixed early Drosophila embryos. Reconstruction showed that the dynamic activation profile of ERK regulates the spatial and temporal extent of the target gene expression. Given that increasing number of studies report the link between changes in ERK kinetics and developmental abnormalities, my project contributed to establish a platform where quantitative regulation of enzyme activity can be studied in vivo.

As a postdoctoral researcher with Professor Michael Levine in the Lewis-Sigler Institute for Integrative Genomics at Princeton University, I applied quantitative image analysis and modeling techniques to explore another critical aspect in development: transcriptional regulation. Transcription is a critical yet a complex process that determines when and where a gene needs to be turned on and off to ensure normal development. While the importance of transcriptional regulation is well acknowledged, complex nature of the process makes it challenging to understand the comprehensive underlying mechanisms of transcriptional regulation.

During the past one year as a postdoctoral researcher, I showed that transcription occurs in a series of sequential stochastic bursts, and these bursts can be readily visualized in living fly embryos. Through quantitative image analysis, I provided evidence that enhancers regulate transcription by modulating the frequency of these bursts, implying that the regulation of bursting frequency is a key parameter of gene control in development. I also showed that a shared enhancer can co-activate two linked reporter genes, arguing against the conventional enhancer-promoter looping models, which would express sequential activation of two reporter genes. The work has contributed to provide new insights on the enhancer-mediated gene regulation in quantitative manner.

Based on these results and my experience in applying quantitative techniques to biological systems, I will further explore the underlying mechanism of transcriptional bursting and the role of enhancer-promoter communication in transcriptional regulation. I will take advantage of the broad range of molecular cloning, optogenetics, and quantitative tools available in the Drosophila system. My initial projects will focus on (1) extracting the properties that comprise minimal unit of transcriptional burst, (2) probing the correlation between the cluster size of RNA polymerase II and the transcriptional burst size, and (3) testing the role of chromosomal loop domains in transcriptional regulation. Given that more and more mutations in the enhancer regions in the genome are found to cause developmental abnormalities, successful implementation of the proposed experiments will shed light on the nature of transcriptional bursts, the relationship between enhancers and bursts, and the effect of enhancer-mediated transcriptional regulation in development.

Teaching Interests:  

I have served as a TA once for the undergraduate Chemical Reaction Engineering course and twice for the graduate level Chemical Reactor Engineering course, both of which are core classes for undergraduate and graduate students in Chemical and Biological engineering at Princeton University, respectively. I received the Air Products Assistant in Instruction Award in 2012, from the graduate Chemical Reactor Engineering class. I have mentored three undergraduate students (2 engineering and 1 molecular biology), and two rotation graduate students in molecular biology.

Selected Publications:

1. Fukaya T*, Lim B*, and Levine M. 2016. Enhancer control of transcriptional bursting. Cell. 2016. dx.doi.org/10.1016/j.cell.2016.05.025 [epub ahead of print]

2. Lim B, Dsilva CJ, Levario TJ, Lu H, Schupbach T, Kevrekidis IG, Shvartsman SY. Dynamics of inductive ERK signaling in the Drosophila embryo. Curr Biol. 2015; 25: 1784-1790.

3. Dsilva CJ*, Lim B*, Lu H, Singer A, Kevrekidis IG, Shvartsman SY. Temporal ordering and registration of images in studies of developmental dynamics. Development. 2015; 142: 1717-1724.

4. Lim B, Samper N, Lu H, Rushlow C, Jimenez G, Shvartsman SY. Kinetics of gene derepression by ERK signaling. Proc Natl Acad Sci U S A. 2013; 110: 10330-10335.

* Equal contribution