This week we profile a recent publication in Scientific Reports from the lab of Dr. Calvin Yip (pictured, fourth from right) at UBC with first author Diana Vasyliuk (third from left).
Can you provide a brief overview of your lab’s current research focus?
Our lab is interested in understanding how cells establish and maintain its gene expression pattern. Eukaryotic genomics DNA exists in a DNA-protein complex known as chromatin. A key mechanism cells regulate chromatin structure and genome accessibility is through post translational modifications of the histone proteins that form the most basic unit of chromatin called the nucleosome. Since the inception of our lab in 2011, we have been using biochemical and structural electron microscopy approaches to study how two conserved histone modifying complexes from budding yeast (SAGA and NuA4) perform their physiological functions. More specifically, we want to find out how the different subunits within these complexes are organized into a single assembly, what are the biological functions of the different subunits, and how the fully-assembled complexes recognize and covalently a chemical group to their nucleosome target.
What is the significance of the findings in this publication?
Advances in cryo-electron microscopy (cryo-EM) technology made it possible to visualize to atomic level details the structural properties of many large, multi-protein complexes in recent years. One major challenge in structural characterization of histone modifying complexes is obtaining sufficient quantities of highly purified material for cryo-EM specimen preparation. The sophisticated composition of these complexes precluded the use of conventional recombinant protein production approaches. Biochemical and structural studies thus far necessitate us to isolate the low-abundant native complexes from yeast cells. Two recent high-resolution cryo-EM studies on yeast SAGA overcome this technical challenge by using large-scale fermentation to culture yeast cells, a strategy that is not easily accessible. In our Scientific Reports paper, we describe a method to procedure high-quality cryo-EM specimens from substantially less purified yeast SAGA and demonstrated that we can obtain a structure of this complex at similar high resolution. We feel that our workflow would democratize cryo-EM investigation of SAGA and other low abundant histone modifying complexes. SAGA and many histone modifying complexes are dynamic assemblies that adopt different conformations. In the second part of our paper, we reported a systematic analysis of SAGA’s conformational landscape using a new machine learning-based algorithm called cryoDRGN. We worked closely with the developer of this program (Dr. Ellen Zhong and Joey Davis at MIT). Results from this in silico analysis revealed that different parts of the multimodular SAGA complex move in a coordinated fashion as opposed to independently.
What are the next steps for this research?
The next step of this research is to find out if the different conformations adopted by SAGA represents different functional states of this complex.
If you’d like to mention your funding sources, please list them.
This research was supported by a Discovery Grant from NSERC to our group. It was also funded by a Globalink Graduate Fellowship Mitacs to my former MSc student Diana Vasyliuk (3rd from the left on the group picture) who is from Ukraine. We would like to dedicate this paper to everyone from her home country.
