Department of Biology

Katharine Abruzzi

Associate Research Professor of Biology

Research Description

Understanding the contribution of post-transcriptional regulation of gene expression in Drosophila circadian rhythms

Organisms, ranging from cyanobacteria to humans, display circadian rhythms, which are time-of-day-dependent physiologies and behaviors controlled by the circadian clock. These occur with an approximately 24-hour period, even in the absence of environmental cues. Circadian clocks are self-sustained, cell-autonomous molecular timers driven by complex transcriptional-translational negative feedback loops in the “clock cells.”  These systems are robust; they maintain 24-hour timing across a range of different temperatures, adapt to seasonal changes in day length, and remain relatively stable with age.   Tight control of circadian gene expression is critical for proper circadian rhythms.  Although the circadian transcriptional control is well studied, it remains unclear how post-transcriptional mechanisms, such as regulated splicing, mRNA export, and translation, contribute to circadian rhythms. 

How does the post-transcriptional regulation of gene expression impact circadian rhythms?  Do these RNA-centric mechanisms help buffer circadian gene expression from environmental changes? What RNA-binding proteins are involved, and how do they regulate their target mRNAs?    

To address these questions, the lab studies the post-transcriptional regulation of gene expression in the ~230 circadian neurons of the Drosophila melanogaster brain.   Transcriptome studies, together with ribosome profiling from these neurons, provide a picture of mRNA splicing, nuclear retention, and translation within these specialized neurons.  In addition, these neurons are also easily genetically manipulated, which allows us to test the role of individual mRNA regulators and their effects on gene expression. 

Developing new technologies to probe post-transcriptional gene regulation in small numbers of neurons.

To examine post-transcriptional gene expression in the ~230 neurons in the Drosophila brain, methods are needed that will work on a microscale to profile mRNAs undergoing translation and identify targets of RNA-binding proteins.   Although these methods are developed for our work in Drosophila, they can be applied to any system where minimal numbers of cells (500-2000) need to be assayed.   In 2016, we developed a genetic method for identifying targets of RNA-binding proteins, called Targets of RNA-binding proteins identified by editing (TRIBE).  We are currently working on a variation of TRIBE, which uses nanobodies to bring the adenosine deaminase ADAR to the RBP of interest, thereby marking target mRNAs with editing sites.  This assay can be performed both in vivo and in vitro, and it works with both tissue culture cells and small numbers of neurons.