Description of Research Expertise

Research Interests

We are interested in understanding how the dynamics of fundamental cellular processes are fine-tuned in developing cells; and apply single-cell imaging and sequencing approaches to uncover principles that drive cell identity establishment and how these can be dysregulated in disease states.

Keywords

Gene regulation, development, cell fate programming, transcriptomics, single-cell imaging

Research Details

In rapidly growing and dividing cells, precise spatio-temporal coordination of basic processes such as transcription and DNA replication is essential for cellular decision making. We use the C. elegans embryo as a model to capture and quantify the dynamics of these processes during developmental cell fate programming. C. elegans embryonic development is invariant, proceeding through highly reproducible division patterns, resulting in an identical set of 558 terminal cells at the time of hatching. We can track the development of each individual cell, identify lineage trajectories, and characterize detailed fate changes in mutant and perturbed individuals, allowing us to directly link molecular dysregulation with developmental defects.

Gene expression programs that control when genes are turned ON are central to cellular programing. The steps involved in these programs are complex and dynamic, occurring in a crowded nuclear space. We are working towards systematically investigating each step and examining their impact on cellular fate decisions in individual cells. Current projects include looking at how the spatial organization and the different stages of transcription contribute to overall dynamics and mRNA accumulation, studying the patterns of replication origin firing and its role in preventing replication-transcription conflicts, connecting mechanisms that buffer transcription noise to invariant fate decisions, and generating humanized C. elegans to investigate the molecular basis of transcription-associated developmental disorders.

Rotation Projects

(1) Contributions of different transcription steps to total RNA dynamics. Test the impact of initiation (using CRISPR, synthetic arrays), elongation (DRB-seq, mutants) and spatial organization (imaging) to mRNA output and developmental outcomes

(2) Can we connect noisy transcription to specific fate defects? Developing combined live RNA imaging (MS2 or RNAi-based) and lineage tracing methods (confocal imaging followed by automated lineage analysis) to investigate mechanisms that buffer transcription noise and promote high-fidelity fate decisions

(3) Coupling cell size to transcription dynamics. Test the hypothesis that cell size might control transcription rates of cell fate regulators using RNAi and degron alleles to manipulate cell size and characterize transcriptome changes by single-cell RNA sequencing and single molecule FISH.

(4) Understanding variable expressivity and penetrance using worm models of human transcription-associated developmental disorders. Mutations in gene associated with general transcription factors show a range of phenotypes, but the molecular mechanisms are not known. By generating humanized worms and knocking-in a human variant of interest, we can connect transcriptome changes with cell fate defects.


(5) Examining replication-transcription conflicts in the rapidly dividing embryo. Mapping the dynamics of replication origin firing in connection with high-rate transcription of cell fate regulators.