![]() ![]() Much of the genome lies close to a regulatory event: 95% of the genome lies within 8 kilobases (kb) of a DNA–protein interaction (as assayed by bound ChIP-seq motifs or DNase I footprints), and 99% is within 1.7 kb of at least one of the biochemical events measured by ENCODE. The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.Together, these efforts reveal important features about the organization and function of the human genome, summarized below. We integrate results from diverse experiments within cell types, related experiments involving 147 different cell types, and all ENCODE data with other resources, such as candidate regions from genome-wide association studies (GWAS) and evolutionarily constrained regions. Here we describe the production and initial analysis of 1,640 data sets designed to annotate functional elements in the entire human genome. The advent of more powerful DNA sequencing technologies now enables whole-genome and more precise analyses with a broad repertoire of functional assays. In a pilot phase covering 1% of the genome, the ENCODE project annotated 60% of mammalian evolutionarily constrained bases, but also identified many additional putative functional elements without evidence of constraint 2. Comparative genomic studies suggest that 3–8% of bases are under purifying (negative) selection 4, 5, 6, 7, 8 and therefore may be functional, although other analyses have suggested much higher estimates 9, 10, 11. Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure). ![]() The Encyclopedia of DNA Elements (ENCODE) project aims to delineate all functional elements encoded in the human genome 1, 2, 3. Such analyses can also provide comprehensive views of the organization and variability of genes and regulatory information across cellular contexts, species and individuals. Systematic analyses of transcripts and regulatory information are essential for the identification of genes and regulatory regions, and are an important resource for the study of human biology and disease. Despite intensive study, especially in identifying protein-coding genes, our understanding of the genome is far from complete, particularly with regard to non-coding RNAs, alternatively spliced transcripts and regulatory sequences. The human genome sequence provides the underlying code for human biology. ENCODE Encyclopedia of DNA Elements /encode ![]()
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