IGSB Fellow Marcelo Nobrega-  A Fishfinder for the “Junk DNA” Seas

February 22, 2010

A Fishfinder for the “Junk DNA” Seas

In a way, the Human Genome Project had it easy. Sure, mapping the roughly 23,000 genes active in humans was one of the most important scientific achievements of all time, but those genes are only part of the story. In fact, the protein-coding sequences only occupy about 1.5% of the roughly 3 billion base pairs present in human DNA; the actual genes are small islands afloat in a vast sea of largely unknown sequences.

Those mysterious stretches were once referred to dismissively as “junk DNA,” as scientists presumed that all those base pairs between the genes must be largely the cold leftovers of evolution - sequences that may have been important to other species but had lost their utility in humans. But now that we have a pretty reliable map of our 23,000 genes, it’s become apparent that rich treasure lies hidden in the junk DNA. Since all cells of the human body share the same DNA, a set of instructions must be present to direct Cell A to become a neuron and Cell B to become a heart cell and so forth. Increasingly, these “switches” are understood to be key to both construction of a functioning body and the ways that process can break down in genetic diseases. But finding those switches is no easy task.

“These sequences are literally in the middle of nowhere, these tiny things in a sea of anonymous sequences,” said Marcelo Nobrega, assistant professor of human genetics at the University of Chicago. “The question was: How are you going to find those?”

In a recent paper in the journal Genome Research, a team of researchers from the University of Chicago and the National Institutes of Health may have made that search much easier. Just as modern fishermen use computerized fishfinders to help them spot prize catches in the waters below, Nobrega, Ivan Ovcharenko and colleagues have developed a computer tool to scan the DNA depths for the tiny switches important for cell determination. First demonstrating the model’s usefulness by tracking down sequences important for heart development, the authors said the method can be used to sniff out molecular switches that control the fate of every kind of cell, in humans or other organisms.

“The Human Genome Project gave us a book with 3 billion letters, of which 3 million are known words,” said Nobrega, assistant professor of human genetics at the University of Chicago. “But that doesn’t tell the story, and in the time that it’s taking to unravel the other things hidden in genome, we’re learning just how complicated it’s going to be.”