Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Abstract

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

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Affiliated Institutions

• University of California, Santa Cruz US
• University of Massachusetts Chan Medical School US
• Agency for Science, Technology and Research SG
• Fraunhofer Society DE
• University of Virginia US
• Allen Institute for Brain Science US
• Stanford University US
• Yale University US
• Thermo Fisher Scientific (Israel) IL
• University of Geneva CH
• University of Washington US
• Boston University US
• Universitat de Barcelona ES
• Allen Institute US
• Duke University US
• University of North Carolina at Chapel Hill US
• Seattle University US
• Harvard University Press US
• Leipzig University DE
• Universitat Pompeu Fabra ES
• University of Lausanne CH
• National Institutes of Health US
• University of Vienna AT

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