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Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, Niblett D, Otto T, Pettett R, Seemann S, Thompson C, West T, Rogers J, Olek A, Berlin K, Beck S. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006; 38:1378-85. [PMID: 17072317 PMCID: PMC3082778 DOI: 10.1038/ng1909] [Citation(s) in RCA: 933] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 09/18/2006] [Indexed: 12/17/2022]
Abstract
DNA methylation is the most stable type of epigenetic modification modulating the transcriptional plasticity of mammalian genomes. Using bisulfite DNA sequencing, we report high-resolution methylation profiles of human chromosomes 6, 20 and 22, providing a resource of about 1.9 million CpG methylation values derived from 12 different tissues. Analysis of six annotation categories showed that evolutionarily conserved regions are the predominant sites for differential DNA methylation and that a core region surrounding the transcriptional start site is an informative surrogate for promoter methylation. We find that 17% of the 873 analyzed genes are differentially methylated in their 5' UTRs and that about one-third of the differentially methylated 5' UTRs are inversely correlated with transcription. Despite the fact that our study controlled for factors reported to affect DNA methylation such as sex and age, we did not find any significant attributable effects. Our data suggest DNA methylation to be ontogenetically more stable than previously thought.
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MESH Headings
- 5' Untranslated Regions
- Adult
- Age Factors
- Aged
- Animals
- Chromosomes, Human, Pair 20/genetics
- Chromosomes, Human, Pair 20/metabolism
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 22/metabolism
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 6/metabolism
- CpG Islands
- DNA Methylation
- Epigenesis, Genetic
- Evolution, Molecular
- Female
- Humans
- Male
- Mice
- Middle Aged
- Organ Specificity
- Promoter Regions, Genetic
- Sex Characteristics
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- Florian Eckhardt
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Joern Lewin
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Rene Cortese
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Vardhman K. Rakyan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - John Attwood
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Matthias Burger
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - John Burton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Tony V. Cox
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Rob Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas A. Down
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Roger Horton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Kevin Howe
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David K. Jackson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Christoph Koenig
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Jennifer Liddle
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David Niblett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Otto
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Roger Pettett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Stefanie Seemann
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | | | - Tony West
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Alex Olek
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Kurt Berlin
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
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Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR. A physical map of the mouse genome. Nature 2002; 418:743-50. [PMID: 12181558 DOI: 10.1038/nature00957] [Citation(s) in RCA: 251] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.
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Affiliation(s)
- Simon G Gregory
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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