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

Birney, Ewan and Pachter, Lior (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 0028-0836. PMCID PMC2212820. doi:10.1038/nature05874.

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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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Pachter, Lior0000-0002-9164-6231
Additional Information:© 2007 Macmillan Publishers Limited. Received 2 March 2007; Accepted 23 April 2007. We thank D. Leja for providing graphical expertise and support. Funding support is acknowledged from the following sources: National Institutes of Health, The European Union BioSapiens NoE, Affymetrix, Swiss National Science Foundation, the Spanish Ministerio de Educación y Ciencia, Spanish Ministry of Education and Science, CIBERESP, Genome Spain and Generalitat de Catalunya, Ministry of Education, Culture, Sports, Science and Technology of Japan, the NCCR Frontiers in Genetics, the Jérôme Lejeune Foundation, the Childcare Foundation, the Novartis Foundations, the Danish Research Council, the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the Wellcome Trust, the Howard Hughes Medical Institute, the Bio-X Institute, the RIKEN Institute, the US Army, National Science Foundation, the Deutsche Forschungsgemeinschaft, the Austrian Gen-AU program, the BBSRC and The European Molecular Biology Laboratory. We thank the Barcelona SuperComputing Center and the NIH Biowulf cluster for computer facilities. The Consortium thanks the ENCODE Scientific Advisory Panel for their advice on the project: G. Weinstock, M. Cherry, G. Churchill, M. Eisen, S. Elgin, J. Lis, J. Rine, M. Vidal and P. Zamore. The author declares no competing financial interests.
Issue or Number:7146
PubMed Central ID:PMC2212820
Record Number:CaltechAUTHORS:20170307-121815071
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74855
Deposited By: George Porter
Deposited On:07 Mar 2017 21:24
Last Modified:15 Nov 2021 16:28

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