The ENCODE (ENCyclopedia Of DNA Elements) Project The ENCODE Project Consortium

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (E1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome. With the complete human genome sequence now in hand (1–3), we face the enormous challenge of interpreting it and learning how to use that information to understand the biology of human health and disease. The ENCyclopedia Of DNA Elements (ENCODE) Project is predicated on the belief that a comprehensive catalog of the structural and functional components encoded in the human genome sequence will be critical for understanding human biology well enough to address those fundamental aims of biomedical research. Such a complete catalog, or Bparts list,[ would include protein-coding genes, non–protein-coding genes, transcriptional regulatory elements, and sequences that mediate chromosome structure and dynamics; undoubtedly, additional, yet-to-bedefined types of functional sequences will also need to be included. To illustrate the magnitude of the challenge involved, it only needs to be pointed out that an inventory of the best-defined functional components in the human genome— the protein-coding sequences—is still incomplete for a number of reasons, including the fragmented nature of human genes. Even with essentially all of the human genome sequence in hand, the number of protein-coding genes can still only be estimated (currently 20,000 to 25,000) (3). Non–protein-coding genes are much less well defined. Some, such as the ribosomal RNA and tRNA genes, were identified several decades ago, but more recent