Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. / Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Kuehn, Michael S; Taylor, Christopher M; Neph, Shane; Koch, Christoph M; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A; Andrews, Robert M; Flicek, Paul; Boyle, Patrick J; Cao, Hua; Carter, Nigel P; Clelland, Gayle K; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C; Dorschner, Michael O; Fiegler, Heike; Giresi, Paul G; Goldy, Jeff; Hawrylycz, Michael; Haydock, Andrew; Humbert, Richard; James, Keith D; Johnson, Brett E; Johnson, Ericka M; Frum, Tristan T; Rosenzweig, Elizabeth R; Karnani, Neerja; Lee, Kirsten; Lefebvre, Gregory C; Navas, Patrick A; Neri, Fidencio; Parker, Stephen C J; Sabo, Peter J; Sandstrom, Richard; Sandelin, Albin; Pedersen, Jakob Skou; ENCODE Project Consortium; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute.
I: Nature, Bind 447, Nr. 7146, 2007, s. 799-816.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
AU - Birney, Ewan
AU - Stamatoyannopoulos, John A
AU - Dutta, Anindya
AU - Guigó, Roderic
AU - Gingeras, Thomas R
AU - Margulies, Elliott H
AU - Weng, Zhiping
AU - Snyder, Michael
AU - Dermitzakis, Emmanouil T
AU - Thurman, Robert E
AU - Kuehn, Michael S
AU - Taylor, Christopher M
AU - Neph, Shane
AU - Koch, Christoph M
AU - Asthana, Saurabh
AU - Malhotra, Ankit
AU - Adzhubei, Ivan
AU - Greenbaum, Jason A
AU - Andrews, Robert M
AU - Flicek, Paul
AU - Boyle, Patrick J
AU - Cao, Hua
AU - Carter, Nigel P
AU - Clelland, Gayle K
AU - Davis, Sean
AU - Day, Nathan
AU - Dhami, Pawandeep
AU - Dillon, Shane C
AU - Dorschner, Michael O
AU - Fiegler, Heike
AU - Giresi, Paul G
AU - Goldy, Jeff
AU - Hawrylycz, Michael
AU - Haydock, Andrew
AU - Humbert, Richard
AU - James, Keith D
AU - Johnson, Brett E
AU - Johnson, Ericka M
AU - Frum, Tristan T
AU - Rosenzweig, Elizabeth R
AU - Karnani, Neerja
AU - Lee, Kirsten
AU - Lefebvre, Gregory C
AU - Navas, Patrick A
AU - Neri, Fidencio
AU - Parker, Stephen C J
AU - Sabo, Peter J
AU - Sandstrom, Richard
AU - Sandelin, Albin
AU - Pedersen, Jakob Skou
AU - ENCODE Project Consortium
AU - NISC Comparative Sequencing Program
AU - Baylor College of Medicine Human Genome Sequencing Center
AU - Washington University Genome Sequencing Center
AU - Broad Institute
AU - Children's Hospital Oakland Research Institute
N1 - Keywords: Chromatin; Chromatin Immunoprecipitation; Conserved Sequence; DNA Replication; Evolution, Molecular; Exons; Genome, Human; Genomics; Heterozygote; Histones; Humans; Pilot Projects; Protein Binding; RNA, Messenger; RNA, Untranslated; Regulatory Sequences, Nucleic Acid; Transcription Factors; Transcription Initiation Site; Transcription, Genetic; Variation (Genetics)
PY - 2007
Y1 - 2007
N2 - 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.
AB - 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.
U2 - 10.1038/nature05874
DO - 10.1038/nature05874
M3 - Journal article
C2 - 17571346
VL - 447
SP - 799
EP - 816
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7146
ER -
ID: 4960853