We congratulate Dr. John Stamatoyannopoulos for receiving the UW Alumi Early Achievement Award.
Dr. Stamatoyannopoulos led the Encyclopedia of DNA Elements (ENCODE) Consortium, an international project aimed at elucidating the genomes dark matter responsible for fine-tuning genetic function. This project has wide- ranging implications for genetics, development and stem-cell studies and has drawn worldwide attention. Learn more about Stamatoyannopoulos work in UW Medicine magazine.
More from the UW Medicine magazine -
The sheer volume of data allowed an incredibly high-resolution look at gene regulation. When the project began, for example, the researchers could examine what was happening at the level of several hundred base pairs, the chemical bases that form DNA. By 2010, they realized that they could see activity all the way down to single base pairs. This advance enabled them to detect more than 8.5 million docking slots for different individual regulatory proteins on the DNA of the living genome; these regulatory proteins recognize specific words written in the DNA sequence. Many of the words were compatible with known regulatory proteins, but most had not been seen before.
We exposed a whole new universe of codes and instructions that the genome is using to control genes, says Stamatoyannopoulos. And the evaluation system theyve built is applicable for different kinds of cells. In fact, theyve now produced detailed descriptions of regulatory protein docking for over 50 cell types, and used these data to understand showing how instructions in regulatory DNA direct gene activity.
Now we can really see how the machine is working at a level that we couldnt before, says Stamatoyannopoulos.
On implications for curing disease -
As Stamatoyannopoulos puts it, there usually wont be a simple solution to illness: one gene for X disease, or another gene for Y disease. Rather, ENCODE ushers in an era in which many diseases are understood to be the result of complex interactions among regulatory DNA regions and the genes they switch on and off.
Adding to the complexity is proximity, or lack of it. It seems logical to assume that genes would be affected by the regulatory regions closest to them. To examine this assumption, Stamatoyannopoulos group developed an approach for connecting regulatory regions to the genes they control. Surprisingly, they found that the great majority of genes were far away from their controlling regulatory regions.
This finding has major implications for piecing together the genetic causes of disease.
On implications for real science -