Defining functional DNA elements in the human genome

With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional r...

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Published in	Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 17; pp. 6131 - 6138
Main Authors	Kellis, Manolis, Wold, Barbara, Snyderd, Michael P., Bernstein, Bradley E., Kundaje, Anshul, Marinov, Georgi K., Ward, Lucas D., Birney, Ewan, Crawford, Gregory E., Dekker, Job, Dunham, Ian, Elnitski, Laura L., Farnham, Peggy J., Feingold, Elise A., Gerstein, Mark, Giddings, Morgan C., Gilbert, David M., Gingeras, Thomas R., Green, Eric D., Guigo, Roderic, Hubbard, Tim, Kent, Jim, Lieb, Jason D., Myerst, Richard M., Pazin, Michael J., Ren, Bing, Stamatoyannopoulos, John A., Weng, Zhiping, White, Kevin P., Hardison, Ross C.
Format	Journal Article
Language	English
Published	United States National Academy of Sciences 29.04.2014 National Acad Sciences
Subjects	binding sites Biochemistry Biological Evolution Biological Sciences chromatin Deoxyribonucleic acid Disease - genetics DNA DNA - genetics Evolution Evolutionary genetics Genes Genome, Human - genetics Genomes Genomics human diseases Human genetics Human genome Human subjects Humans messenger RNA nucleotide sequences PERSPECTIVE Regulatory Sequences, Nucleic Acid - genetics RNA Software transcription factors
Online Access	Get full text
ISSN	0027-8424 1091-6490 1091-6490
DOI	10.1073/pnas.1318948111

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Abstract	With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease.
AbstractList	With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease. With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease. [PUBLICATION ABSTRACT] With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease.With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease.
Author	Myerst, Richard M. Snyderd, Michael P. Kent, Jim Wold, Barbara Hardison, Ross C. White, Kevin P. Gilbert, David M. Birney, Ewan Kellis, Manolis Crawford, Gregory E. Kundaje, Anshul Farnham, Peggy J. Gingeras, Thomas R. Dunham, Ian Green, Eric D. Giddings, Morgan C. Stamatoyannopoulos, John A. Pazin, Michael J. Ren, Bing Elnitski, Laura L. Gerstein, Mark Weng, Zhiping Dekker, Job Bernstein, Bradley E. Marinov, Georgi K. Feingold, Elise A. Guigo, Roderic Lieb, Jason D. Hubbard, Tim Ward, Lucas D.
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/24753594$$D View this record in MEDLINE/PubMed
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Snippet	With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and...
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StartPage	6131
SubjectTerms	binding sites Biochemistry Biological Evolution Biological Sciences chromatin Deoxyribonucleic acid Disease - genetics DNA DNA - genetics Evolution Evolutionary genetics Genes Genome, Human - genetics Genomes Genomics human diseases Human genetics Human genome Human subjects Humans messenger RNA nucleotide sequences PERSPECTIVE Regulatory Sequences, Nucleic Acid - genetics RNA Software transcription factors
Title	Defining functional DNA elements in the human genome
URI	https://www.jstor.org/stable/23772466 http://www.pnas.org/content/111/17/6131.abstract https://www.ncbi.nlm.nih.gov/pubmed/24753594 https://www.proquest.com/docview/1523948285 https://www.proquest.com/docview/1520343603 https://www.proquest.com/docview/1534857255 https://www.proquest.com/docview/1803095650 https://pubmed.ncbi.nlm.nih.gov/PMC4035993
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