Washington, Dec 12 : Hopkins researchers have found that regulatory DNA which aids in turning the gene on and off and contributes to inherited diseases like Parkinson's or mental disorders may be more abundant than previously thought.
Hopkins researchers have found that regulatory DNA which aids in turning the gene on and off and contributes to inherited diseases like Parkinson's or mental disorders may be more abundant than previously thought.
The research was carried out by a team led by Andrew McCallion, Ph.D., an assistant professor in the McKusick-Nathans Institute of Genetic Medicine.
After conducting an exhaustive analysis of the DNA sequence around a gene required for neuronal development, it was found that current computer programs that scan the genome in order to find regulatory DNA could miss more than 60 pct of these important DNA regions.
Existing methods find regulatory sequences through comparing DNA belonging to distantly related species, based on the theory that functionally important regions will be more similar in sequence than non-functional regions.
"The problem with this approach, we have discovered, is that it's often throwing the baby out with the bath water. So while we believe sequence conservation is a good method to begin finding regulatory elements, to fully understand our genome we need other approaches to find the missing regulatory elements," said McCallion.
McCallion had suspected that using sequence conservation would overlook some regulatory DNA, but to see how much, he set up a small pilot project looking at the phox2b (involved in forming part of the brain associated with stress response as well as nerves that control the digestive system) gene. This gene was chosen because of its small size and his interest in nerve development.
The researchers created what they call a "tiled path," cutting up the DNA sequence around the phox2b gene into small pieces, and then inserted each piece into zebrafish embryos along with a gene for a fluorescent protein.
If a phox2b fragment was a regulatory element, then it would cause the protein to glow. By watching the growing fish embryos - which have the advantage of being transparent - the researchers could see which pieces were regulators.
A total of 17 discrete DNA segments were uncovered, having the ability to make fish glow in the right cells.
Then the entire region around the phox2b gene was analyzed using the five commonly used computer programs that compute sequence conservation; these established methods picked up only 29 pct to 61 pct of the phox2b regulators McCallion identified in the zebrafish experiments.
"Our data supports the recent NIH encyclopedia of DNA elements project, which suggests that many DNA sequences that bind to regulatory proteins are in fact not conserved," said McCallion.
He added: "I hope this pilot shows that these types of analyses can be worthwhile, especially now that they can be done quickly and easily in zebrafish."
He is now planning a larger study of other neuronal genes.
"I think we are only starting to realize the importance and abundance of regulatory elements; by regulating the gene activity in each cell they help create the diverse range of cell types in our body," he said.
This study was reported online this week in Genome Research. (ANI)
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