The findings are being published today in the scientific journal Nature Physics .

In living cells, DNA-binding proteins regulate the activity of various genes so that different cells carry out the right tasks at the right time. For this to work, the DNA-binding proteins need to find the right DNA site sufficiently quickly. The research team behind the new study has previously succeeded in determining that it takes only a few minutes for an individual protein molecule to look through the millions of nearly identical binding alternatives and find the right place to bind. This is nevertheless slower than what is predicted by the established theoretical model for how DNA-binding proteins find their way to the proper place by alternating between diffusing in the cell cytoplasm and along DNA strands.

"By also taking into consideration the fact that there are many obstacles in the way when proteins are to diffuse along DNA strands, we can now calculate more exactly how long it takes them to find their way," says Johan Elf, associate professor of molecular biotechnology at the Center for Bioinformatics.

Besides offering a more precise prediction regarding the time needed to find the right site on DNA, the new theoretical model explains why there is an optimal total concentration of DNA-binding proteins. If there were more, it would simply be impossible for them to find a binding place in a reasonable time, since the proteins would be in each other's way. If there were fewer it would go slower as well, since not enough proteins would be searching. Finally, the new model provides an explanation why so many DNA-binding proteins also bind auxiliary binding sites close to the regulatory site, thus forming DNA loops. It turns out that this can shorten the time to find the right sites.

"This more detailed understanding of gene regulation is important, since it can ultimately provide a better understanding of diseases that occur as a result of problems in the control functions of cells, such as in cancer" says Johan Elf.

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To discover ESRP1 and ESRP2, the team used a high-throughput genetic screen for rare proteins developed by collaborator and co-author John B. Hogenesch, PhD, Associate Professor of Pharmacology, an innovator in the use of these types of screens. In addition, Claude Warzecha, a graduate student in the Carstens lab, played a key role in the completion of the screen.

The screen consists of about 15,000 different cDNAs (DNA that has been synthesized from messenger RNAs) that each express a different gene and are arrayed on plates so that each well of the plate expresses only one individual gene product. The Carstens lab developed a splicing "reporter" that makes cells express a firefly luciferase gene and "glow" when it is spliced in the epithelial cell pattern. Cells with this reporter were individually placed over wells containing each cDNA and cells that "glowed, indicated those cDNAs that produced proteins that promoted the epithelial splicing program. It was from this screen that ESRP1 and ESRP2 emerged.

In ongoing work, the team found that ESRP1 and ESRP2 are critical for epithelial-specific splicing of many other genes in addition to FGFR2. Several of the proteins made from these RNAs also have different functions that either help cells to stay attached in place or to promote local invasion of cancer cells that are capable of traveling to distant sites. The team is also engineering mice in which the genes for ESRP1 and 2 can be selectively "knocked-out" so that they can further study the importance of these two proteins during development as well as in disease. In addition, studies are planned to use the same splicing reporter system to screen for drugs that might restore the epithelial pathway and interfere with metastasis and fibrosis.

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