The modENCODE team took on an enormous task: to create a detailed picture of this molecular dance. For the past five years, hundreds of biologists have been recording DNA activity in flies and worms, and systematically comparing the results to what they see in humans.

To study genes in humans, the scientists focused on a wide variety of cells, like neurons, blood cells and liver cells. In the experiments on flies and worms, the scientists examined the entire bodies of the animals as they matured from eggs.

The scientists cataloged the parts of the genome that cells were using. They also mapped the histone marks and located the transcription factors latching onto the DNA. Because the scientists used the same methods to gather data from all three species, they were able to compare them on a scale never before attempted.

Flies, worms and humans come from distant branches on the evolutionary tree. The last common ancestor lived 700 million years ago. Despite the tremendous differences among the three species, the modENCODE team found some striking parallels in the workings of their DNA.

In all three, it turned out, many genes tended to turn on and off in the same pattern, following a predictable rhythm. All told, the researchers found 16 such sets of genes, each containing hundreds of genes working together. While it’s not clear yet what these genes are doing in all three species, the scientists did observe that a dozen clusters were especially active at some stages of development in the worm and the fly. They may be essential for transforming an egg into an adult animal.

The scientists also found that histone marks control DNA in much the same way in all three species. If certain marks were present around a gene, the scientists usually could predict how active it was, whether fly, worm or human.

“The neat thing is that it works — it really works well,” Mark Gerstein of Yale University, a modENCODE team member, said of the group’s predictive model.