Once upon a time, to be a gene, a stretch of DNA had to code for a protein. "That's not true anymore," Carlo Croce told BioWorld Today.

In the Sept, 2007 issue of Cancer Cell, senior author Croce, director of the human cancer genetics program at the Ohio State University, and his colleagues show changes in the transcription levels of so-called ultraconserved regions of the genome in cancer tissue samples. With that finding, Croce said, ultraconserved regions join microRNAs as DNA that "are clearly genes, but do not encode for proteins."

Ultraconserved regions are stretches of DNA of at least 200 base pairs in length that are perfectly identical between mice, rats and humans, meaning that no base pair has been changed within such sequences for at least 85 million years.

The researchers used microarrays to determine the RNA expression levels of nearly 500 ultraconserved sequences in tissue samples from normal tissues and from leukemias, colorectal cancer and liver cancer. Roughly 10 percent of ultraconserved regions were expressed differently in cancer tissue samples than in normal ones.

In colorectal cancers, almost all of the ultraconserved sequences were upregulated, whereas the other cancer types showed both upregulated and downregulated transcription. Croce said that it is too early to speculate on why colorectal cancer might have more upregulation than the other cancer types his team studied, but that the finding shows the patterns can be useful in clinical practice.

"For sure, what we are seeing is cell-type and tissue-specific," Croce said. And so "we can certainly use the profile for diagnostic purposes, and possibly for prognostic purposes." Therapeutic approaches to normalizing the expression levels are also a possibility.

When the researchers knocked down one specific upregulated ultraconserved region in colorectal cancer cells using short interfering RNAs, they were able to induce apoptosis in the cancer cells. At least some of the ultraconserved sequences interacted with microRNAs, which recently have been implicated in some cancers. While the functional significance of the finding for cancer is not yet clear, Croce said the data suggested that "microRNA can regulate not only coding genes, but also ultraconserved RNA."

Croce's team also investigated the genomic location of the ultraconserved regions and found that like microRNAs, they tend to lie in fragile regions of the genome - a surprising finding, given that perfect sequence conservation for tens of millions of years would be harder to achieve in unstable regions of the genome than elsewhere.

At first glance, the findings reported in Cancer Cell are at odds with another recent paper. In the August 2007 issue of PLoS Biology, scientists from Lawrence Berkeley National Laboratory and the Department of Energy Joint Genome Institute reported that knocking out several ultraconserved regions had little to no effect on mice, which were described in the paper as "viable and fertile, and failed to reveal any critical abnormalities when assayed for a variety of phenotypes including growth, longevity, pathology and metabolism." When asked to comment, Croce said that knockouts can have fairly mild phenotypes, and that the research published in PLoS Biology - as indeed all research on ultraconserved elements, which were first described only in 2004 - is still in its early stages.

"We will see a lot of knockouts" of ultraconserved regions over the next few years, he said. And some of them "certainly" will have phenotypes.