Using technology he helped develop, Vanderbilt University scientist Bryan Venters, Ph.D., has shed new light on the "dark matter" of the genome and has begun to explore a possible new approach to treating cancer.
"Clarity is everything," said Venters, assistant professor of Molecular Physiology and Biophysics who further developed the high-resolution technology as a postdoctoral fellow in the lab of Frank Pugh, Ph.D., at Pennsylvania State University before moving to Vanderbilt in January.
Venters and Pugh are co-authors of a paper published this week in the journal Nature that describes their finding.
Much of the DNA of the human genome has been called "dark matter" because only a tiny fraction, about 3 percent, makes up the approximately 20,000 protein-coding genes that are transcribed into RNA copies, and then translated into proteins.
Other parts of the genome are transcribed into non-coding RNA, presumably to perform other functions, but until recently the origin of this non-coding RNA was unknown.
Now, with a technique called ChIP-exo developed at Penn State that identifies protein-DNA interactions at near base-pair resolution, Venters and Pugh have shown that so-called transcription initiation complexes drive much of the non-coding transcription occurring throughout the genome.
In a model leukemia cell line, they discovered about 150,000 complexes along non-coding stretches of the DNA the most ever discovered. This suggests, they concluded, that "pervasive non-coding transcription is promoter-specific, regulated, and not that much different from coding transcription (of genes)."
Venters compared the technique to the highly sensitive satellite cameras that enable web-based map applications to zoom in from a continental view to street level, "and tell house from house."
Now he is using the technique to study "the contribution that the JAK-STAT (signaling) pathway makes to the
|Contact: Craig Boerner|
Vanderbilt University Medical Center