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

Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Albin Sandelin; Jakob Skou Pedersen; 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

doi:10.1038/nature05874

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

Ewan Birney, John A Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R Gingeras, Elliott H Margulies, Zhiping Weng, Michael Snyder, Emmanouil T Dermitzakis, Robert E Thurman, Michael S Kuehn, Christopher M Taylor, Shane Neph, Christoph M Koch, Saurabh Asthana, Ankit Malhotra, Ivan Adzhubei, Jason A Greenbaum, Robert M Andrews, Paul FlicekPatrick J Boyle, Hua Cao, Nigel P Carter, Gayle K Clelland, Sean Davis, Nathan Day, Pawandeep Dhami, Shane C Dillon, Michael O Dorschner, Heike Fiegler, Paul G Giresi, Jeff Goldy, Michael Hawrylycz, Andrew Haydock, Richard Humbert, Keith D James, Brett E Johnson, Ericka M Johnson, Tristan T Frum, Elizabeth R Rosenzweig, Neerja Karnani, Kirsten Lee, Gregory C Lefebvre, Patrick A Navas, Fidencio Neri, Stephen C J Parker, Peter J Sabo, Richard Sandstrom, Albin Sandelin, Jakob Skou Pedersen, 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

Functional Genomics

3770 Citations (Scopus)

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.

Original language	English
Journal	Nature
Volume	447
Issue number	7146
Pages (from-to)	799-816
Number of pages	17
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature05874
Publication status	Published - 2007

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Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., ... Children's Hospital Oakland Research Institute (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816. https://doi.org/10.1038/nature05874

Birney, E, Stamatoyannopoulos, JA, Dutta, A, Guigó, R, Gingeras, TR, Margulies, EH, Weng, Z, Snyder, M, Dermitzakis, ET, Thurman, RE, Kuehn, MS, Taylor, CM, Neph, S, Koch, CM, Asthana, S, Malhotra, A, Adzhubei, I, Greenbaum, JA, Andrews, RM, Flicek, P, Boyle, PJ, Cao, H, Carter, NP, Clelland, GK, Davis, S, Day, N, Dhami, P, Dillon, SC, Dorschner, MO, Fiegler, H, Giresi, PG, Goldy, J, Hawrylycz, M, Haydock, A, Humbert, R, James, KD, Johnson, BE, Johnson, EM, Frum, TT, Rosenzweig, ER, Karnani, N, Lee, K, Lefebvre, GC, Navas, PA, Neri, F, Parker, SCJ, Sabo, PJ, Sandstrom, R, Sandelin, A, Pedersen, JS, 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 2007, 'Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.', Nature, vol. 447, no. 7146, pp. 799-816. https://doi.org/10.1038/nature05874

@article{c0d81ba04dc411dd8d9f000ea68e967b,

title = "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.",

author = "Ewan Birney and Stamatoyannopoulos, {John A} and Anindya Dutta and Roderic Guig{\'o} and Gingeras, {Thomas R} and Margulies, {Elliott H} and Zhiping Weng and Michael Snyder and Dermitzakis, {Emmanouil T} and Thurman, {Robert E} and Kuehn, {Michael S} and Taylor, {Christopher M} and Shane Neph and Koch, {Christoph M} and Saurabh Asthana and Ankit Malhotra and Ivan Adzhubei and Greenbaum, {Jason A} and Andrews, {Robert M} and Paul Flicek and Boyle, {Patrick J} and Hua Cao and Carter, {Nigel P} and Clelland, {Gayle K} and Sean Davis and Nathan Day and Pawandeep Dhami and Dillon, {Shane C} and Dorschner, {Michael O} and Heike Fiegler and Giresi, {Paul G} and Jeff Goldy and Michael Hawrylycz and Andrew Haydock and Richard Humbert and James, {Keith D} and Johnson, {Brett E} and Johnson, {Ericka M} and Frum, {Tristan T} and Rosenzweig, {Elizabeth R} and Neerja Karnani and Kirsten Lee and Lefebvre, {Gregory C} and Navas, {Patrick A} and Fidencio Neri and Parker, {Stephen C J} and Sabo, {Peter J} and Richard Sandstrom and Albin Sandelin and Pedersen, {Jakob Skou} and {ENCODE Project Consortium} and {NISC Comparative Sequencing Program} and {Baylor College of Medicine Human Genome Sequencing Center} and {Washington University Genome Sequencing Center} and {Broad Institute} and {Children's Hospital Oakland Research Institute}",

note = "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)",

year = "2007",

doi = "10.1038/nature05874",

language = "English",

volume = "447",

pages = "799--816",

journal = "Nature",

issn = "0028-0836",

publisher = "nature publishing group",

number = "7146",

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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

SN - 0028-0836

VL - 447

SP - 799

EP - 816

JO - Nature

JF - Nature

IS - 7146

ER -

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

Abstract

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