Cells are the fundamental units of life and although they come in a wide range of shapes and sizes, each cell of an organism contains the same number of genes in the cellular DNA. This DNA contains the code for important building blocks of the cell (RNA and protein), and because larger cells require more of these blocks than smaller cells, the DNA must receive information about the number of blocks to generate. This project aims to understand, by experiment, the nature of this exchange of information between DNA and other molecules within the cell. These experiments will reveal whether there are particular genes for which the cell is especially careful about how many building blocks it produces. This project will yield a fundamental quantitative understanding of how cells are able to function despite large differences in size, and will build a connection between the physical context of the cell and the biochemical regulation of the amounts of RNA generated from genes. In addition to training graduate students this project will engage graduate and high-school students to help reimagine how we disseminate scientific information. Web-based technologies will be used in educational outreach as a means to make scientific projects and their results more accessible to both other scientists as well as the general public. Collaborative pairs of graduate students and high school students will transform scientific papers into a series of videos and associated frequently asked questions (FAQs) aimed at making their content more readily understandable. This program will help graduate students develop the skills necessary to present their work, and will encourage high school students to engage with scientific projects at the leading edge of the field.
Cells vary in size throughout the cell cycle, during which they also duplicate their DNA. How do they regulate the concentration of their components in the face of such variability in both cell size and DNA content This project will focus on transcriptional control mechanisms that allow cells to maintain a constant concentration of RNA despite this variability. Cellular volume, cell cycle state, and mRNA abundance will be measured simultaneously in single cells for a panel of endogenous genes using RNA fluorescence in situ hybridization (RNA FISH). For many genes mRNA concentration remains relatively constant regardless of cell cycle and six-fold variations in cellular volume, demonstrating the existence of homeostatic mechanisms in gene expression. It will be determined whether this compensation arises from the control of transcription or of mRNA degradation by using perturbations to transcriptional activity. The nature of the homeostatic mechanisms at work will be characterized in terms of the exact nature of transcriptional changes in different phases of the cell cycle and in cells of different sizes. Cell fusion experiments will be used to test whether cell volume itself can influence gene expression. We will build mathematical models to contextualize and understand our results, in particular focusing on connecting transcriptional parameters to our experimental results. Our results will require a reinterpretation of single cell expression variability and development of new definitions of this transcriptional "noise", and will generate and use deep-sequencing data to provide genome-wide predictions of "noisy" vs. "non-noisy" genes.
This award is supported jointly by the Cellular Dynamics and Function Cluster in the Division of Molecular and Cellular Biosciences and by the Biotechnology, Biochemical and Biomass Engineering Program in the Division of Chemical, Bioengineering, Environmental and Transport Systems.
