Carnegie Mellon
Computational Molecular Biology Symposium

How does a biological cell turn its genes on and off?

Harmen Bussemaker, Department of Biological Sciences, Columbia University

The recent determination of the complete genome sequence of a number of organisms ranging from bacteria to humans has paved the way for a systems-based, quantitative approach to figuring out how a biological cell works. The protein encoded by each gene in the genome is not necessarily present - "expressed" - in the cell, and the distinction between a brain cell and a liver cell in one's body - which have the exact same DNA - results from dramatic differences in global gene expression pattern. It is a modern version of the classic distinction between genotype and phenotype. One of the consequences of the genome projects has been the development of so-called DNA microarrays, devices that can be used to simultaneously measure the expression level of all genes in a cell. The part of the genome that does not code for proteins, often referred to as "junk DNA", contains the key to how genes are turned on and off by the regulatory circuitry of the cell. In this talk we will will discuss two different methods that can be used to decypher this non-coding, regulatory DNA. We first construct a dictionary for non-coding sequences that contains "DNA words" important for gene expression regulation; the method is illustrated by applying it to English text. We then show how fitting a simple mathematical model to DNA microarray data provides useful information about the "state" of a cell.

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The second and fourth images in the header are courtesy the BIODIDAC website.