New Technique Locates Sites of Gene Regulation

A recent paper described the development of a high throughput technique for locating the sites of activity of gene regulators such as CREB (cAMP response element binding protein).

The technique, developed in part by researchers at the Brookhaven National Laboratory (Upton, NY, USA), utilizes restriction enzymes to cut DNA molecules into small fragments of 20 nucleotide bases. The DNA was first allowed to bind to CREB. Then, specific antibodies marked the CREB binding sites, and enzymes were used to generate larger 500 to 1,500 base fragments. After removal of CREB, restriction enzymes were used to obtain the smaller DNA "tag” sequences.

A computer compared the information contained in the tag sequences to sequences in the entire genome of the organism. Using a DNA library derived from rat PC12 cells, the investigators identified about 41,000 genomic signature tags that mapped to unique genomic loci. These findings were published in the December 29, 2004, issue of Cell.

"Our technique gives us a new way to index the code, to find the places where regulators act--where the on/off switches are that determine which genes are at work in different types of cells under different conditions,” said contributing author Dr. John Dunn, a biologist at Brookhaven National Laboratory. "This technique can be applied to any protein that binds to specific sequences in the DNA and promises to be a very useful tool.”



Related Links:
Brookhaven National Laboratory