Targeting transcription: New insights into turning genes on

The 35,000 or so genes within a human cell are something like players on a sports team: If their activity isn’t controlled and coordinated, the result can be disastrous.

So just as coaches tell individual players when to scramble onto the field and when to stay on the bench, molecules called transcription factors prompt particular genes to be active or stay quiet. Transcription factors occur naturally in cells, but researchers have been working to develop artificial transcription factors (ATFs) that can be tailored to regulate particular genes or sets of genes. These molecules can help scientists probe transcription, the first step in the process through which instructions coded in genes are used to produce proteins. And because errors in transcription are linked to diseases ranging from diabetes to cancer, ATFs eventually might also be used to correct those mistakes.

Using a new approach to developing ATFs, University of Michigan assistant professor of chemistry Anna Mapp and coworkers have gained important insights into the workings of gene-activating transcription factors. They recently discovered that the gene-activating power of a transcription factor likely depends on where the factor binds to the cell’s transcriptional machinery, as well as on how tightly it binds. Previously, researchers had thought that binding affinity (tightness) was the main determinant of a gene activator’s potency. Mapp presented the group’s results at the annual meeting of the American Chemical Society in New York today (Sept. 8).

Natural transcription factors typically have two essential parts or modules: a DNA-binding module that homes in on the specific gene to be regulated and a regulatory module that attaches itself to the cell’s transcriptional machinery through a key protein-to-protein interaction and activates or represses the gene.

“When we started thinking about making artificial transcription factors, we knew we needed to find molecules that had that same binding interaction,” Mapp said. Other researchers have created ATFs by shuffling combinations of DNA-binding modules and regulatory modules, typically using regulatory modules that are derived from or resemble natural ones. Mapp’s group took a different approach in hopes of creating smaller ATFs that might be easier to introduce into cells and less likely to be degraded or trigger an immune response—features that would be critical if ATFs are ever to be used in treating disease.

The Michigan team first isolated and purified a protein from the cell’s transcriptional machinery; then they screened large groups of synthetic peptides (short chains of amino acids) for their ability to bind to the protein.

“From that, we got molecules that seem to bind to several different surfaces of the protein,” Mapp said, “and we could use that binding interaction to activate transcription in some cases. So we were able to see for the first time that differences in binding site location may actually affect regulator function.”

The artificial activators are much smaller than most known natural activators. Using the same kind of screening approach, the researchers now plan to search for small organic molecules that are structurally similar to their protein-binding peptides and to combine those molecules with small DNA-binding modules already developed by other researchers, with the goal of creating new ATFs.