Brar Lab Research


 

Explore current projects by clicking on icons below

Click here for more on meiotic sORFs

Click here for more on meiotic sORFs

Click here for more on stress pathways

Click here for more on stress pathways

Click here for more on uORFs and transcript isoforms in meiosis

Click here for more on uORFs and transcript isoforms in meiosis

Click here for more on meiotic translation

Click here for more on meiotic translation

The roles of uORFs and alternate transcript toggling in setting protein levels


Overview

We study the gene regulation underlying meiotic cellular remodeling.

The mechanisms that link cellular differentiation programs and dynamic gene regulation in complex eukaryotic systems remain mysterious. Such programs drive diverse and central biological processes including organismal development, immune function, disease progression, and meiosis. Our lab is focused on the molecular basis for the cellular remodeling accompanying meiosis, the highly conserved process by which gametes are produced.

We study meiosis because it is itself a biologically interesting and important process, but also because it serves as a tractable model for the complex cellular changes that accompany many types of differentiation. We are interested in understanding the fundamental mechanisms by which a cell achieves such changes. Towards this end, we use high-throughput and classical genetic and molecular approaches in budding yeast (S. cerevisiae) to study the role of pervasive short protein synthesis in meiosis, the role of several prominent and diverse stress response pathways in driving cells through the meiotic program, the contribution of regulated transcript toggling to gene regulation, and the modes of translational control that are important in meiotic cells. 


Foundational work for Brar lab

In my post-doctoral studies, I globally probed the regulation of the comprehensive cellular restructuring underlying meiosis. Ribosome profiling, the deep sequencing of ribosome protected mRNA fragments, is a new method that monitors protein synthesis with scale, speed, and accuracy rivaling approaches for mRNA measurement (Ingolia et al., Science 2009). I applied this method to numerous time points through the yeast meiotic program in parallel with mRNA-seq and molecular staging to generate a rich atlas of meiotic events and gene expression and the first high-resolution map of protein synthesis through a developmental program (Brar et al., Science, 2012).

What is ribosome profiling?  Nuclease digestion of translating ribosomes protects only mRNA regions (footprints) being actively decoded by the ribosome ( Steitz, Nature, 1969 ;  Ingolia et al., Science, 2009 ). These footprints can be collected in vivo from cells and sequenced to define coding regions and quantify new protein synthesis. Shown is a comparison of the method with mRNA sequencing, which defines the positions of full transcripts, but cannot specifically identify coding regions.

What is ribosome profiling? Nuclease digestion of translating ribosomes protects only mRNA regions (footprints) being actively decoded by the ribosome (Steitz, Nature, 1969; Ingolia et al., Science, 2009). These footprints can be collected in vivo from cells and sequenced to define coding regions and quantify new protein synthesis. Shown is a comparison of the method with mRNA sequencing, which defines the positions of full transcripts, but cannot specifically identify coding regions.

This study revealed an unprecedented view of the molecular events underlying diverse aspects of meiotic biology and uncovered numerous new and dramatic instances of dynamic translational regulation through meiosis. The effort also yielded several fundamental surprises with broad significance. Projects in the Brar lab are based on exploring the basis and molecular significance of these discoveries. 

A global view of meiotic protein synthesis.  Ribosome footprints over each  S. cerevisiae  gene are shown as columns. Each time point is shown as a row, with 25 meiotic timepoints shown and two mitotic (exponential) controls. Cartoons on the left show progression through meiosis. Note the variety of patterns of regulation of protein synthesis through meiosis, with nearly every gene in the yeast genome expressed and highly regulated. This regulation is mediated by both transcriptional and hundreds of newly identified examples of dramatic translational control. At the right are more detailed views of two genes, with both mRNA and ribosome footprints shown on pooled genome browser tracks. Note that  SPS1  and  SPS2  show similar patterns of mRNA abundance, but very different translation patterns, reflecting just one of these examples of strong translational control.

A global view of meiotic protein synthesis. Ribosome footprints over each S. cerevisiae gene are shown as columns. Each time point is shown as a row, with 25 meiotic timepoints shown and two mitotic (exponential) controls. Cartoons on the left show progression through meiosis. Note the variety of patterns of regulation of protein synthesis through meiosis, with nearly every gene in the yeast genome expressed and highly regulated. This regulation is mediated by both transcriptional and hundreds of newly identified examples of dramatic translational control. At the right are more detailed views of two genes, with both mRNA and ribosome footprints shown on pooled genome browser tracks. Note that SPS1 and SPS2 show similar patterns of mRNA abundance, but very different translation patterns, reflecting just one of these examples of strong translational control.


Ongoing projects in the Brar lab

Discoveries from this study have motivated several research directions in our lab, focused on answering fundamental questions about gene regulation through meiosis.

Questions that interest us are:

1. What are the meiotic roles of the numerous short Open Reading Frames translated specifically in meiotic cells?

2. How do historically defined stress pathways contribute to the dramatic cellular remodeling seen in meiosis?

3. How does regulated toggling between alternate transcripts, together with uORF-mediated translational regulation, contribute to meiotic gene expression?

4. What canonical and noncanonical and translational regulation drive meiotis? What is the impact of protein degradation?

Read more about any of these projects by clicking above or on the icons at the top of the page.