New findings challenge established views about human genome

The ENCyclopedia Of DNA Elements [ENCODE] today published the results of its exhaustive, four-year effort to build a "parts list" of all biologically functional elements in 1 percent of the human genome. The project served as a pilot to test the feasibility of a full-scale initiative to produce a comprehensive catalog of all components of the human genome crucial for biological function. The findings challenge the traditional view of our genetic blueprint as a tidy collection of independent genes, pointing instead to a network in which genes, regulatory elements and other types of DNA sequences interact in complex, overlapping ways. "Our results provide new perspectives on everything from DNA transcription to mammalian evolution. In particular, we gained significant insight into DNA sequences that do not encode proteins, which we knew very little about before." The ENCODE consortium's major findings include the discovery that the majority of human DNA is transcribed into RNA and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a small set of discrete genes, along with a vast amount of "junk" DNA that is not biologically active. The new data indicate that the genome contains little unused sequences; genes are just one of many types of DNA sequences that have a functional impact. They identified many previously unrecognized start sites for transcription and regulatory sequences that contrary to traditional views are located not only upstream but also downstream of transcription start sites. Other surprises have major implications for our understanding of the evolution of genomes. Until recently, researchers had thought that most DNA sequences with important biological function would be constrained by evolution making them likely to be conserved as species evolve. But about half of the functional elements in the human genome do not appear to have been constrained during evolution, suggesting that many species' genomes contain a pool of functional elements that provide no specific benefits in terms of survival or reproduction.