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

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 -