High-resolution analysis of cytosine methylation in ancient DNA

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Llamas, Bastien ^a,b   Holland, Michelle L ^c,e   Chen, Kefei ^a   Cropley, Jennifer E ^c,d   Cooper, Alan ^a   Suter, Catherine M ^c,d  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b FLINDERS UNIVERSITY   (Australia)

^c VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

^e QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; CYTOSINE; DNA;

ANIMAL TISSUE; ARTICLE; BISON PRISCUS; BUFFALO; CATTLE; CONTROLLED STUDY; DNA DETERMINATION; DNA METHYLATION; EPIGENETICS; GENE LOCUS; GENETIC ANALYSIS; GENOME ANALYSIS; GENOME IMPRINTING; HIGH RESOLUTION ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR STABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; RETROPOSON; SEQUENCE ANALYSIS; UPPER PLEISTOCENE; ANIMAL; GENETIC EPIGENESIS; GENETICS; GENOME; MAMMAL; METABOLISM;

BISON PRISCUS; BOVINAE; MAMMALIA;

ANIMALS; BISON; CYTOSINE; DNA METHYLATION; EPIGENESIS, GENETIC; GENOME; MAMMALS; RETROELEMENTS;

EID: 84856023339     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030226     Document Type: Article

References (21)

1. Richards EJ, (2006) Inherited epigenetic variation-revisiting soft inheritance. Nature Reviews Genetics 7: 395-401.
2. Richards EJ, (2008) Population epigenetics. Current Opinion in Genetics and Development 18: 221-226.
3. Jirtle RL, Skinner MK, (2007) Environmental epigenomics and disease susceptibility. Nature Reviews Genetics 8: 253-262.
4. Guerrero-Bosagna C, Sabat P, Valladares L, (2005) Environmental signaling and evolutionary change: can exposure of pregnant mammals to environmental estrogens lead to epigenetically induced evolutionary changes in embryos? Evolution & Development 7: 341-350.
5. Jablonka E, Lamb MJ, (1989) The Inheritance of Acquired Epigenetic Variations. Journal of Theoretical Biology 139: 69-83.
6. Rapp RA, Wendel JF, (2005) Epigenetics and plant evolution. New Phytologist 168: 81-91.
7. Feinberg AP, Irizarry RA, (2010) Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proceedings of the National Academy of Sciences of the United States of America 107: 1757-1764.
8. Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, et al. (2010) Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Research 38: e87.
9. Lindahl T, (1993) Instability and Decay of the Primary Structure of DNA. Nature 362: 709-715.
10. Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M, (2006) DNA methylation: bisulphite modification and analysis. Nature Protocols 1: 2353-2364.
11. Bird A, (2002) DNA methylation patterns and epigenetic memory. Genes and Development 16: 6-21.
12. Hayward BE, Moran V, Strain L, Bonthron DT, (1998) Bidirectional imprinting of a single gene: GNAS1 encodes maternally, paternally, and biallelically derived proteins. Proceedings of the National Academy of Sciences of the United States of America 95: 15475-15480.
13. Huang JM, Kim J, (2009) DNA methylation analysis of the mammalian PEG3 imprinted domain. Gene 442: 18-25.
14. Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, et al. (2007) Novel high-resolution characterization of ancient DNA reveals C&U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Research 35: 5717-5728.
15. Stiller M, Green RE, Ronan M, Simons JF, Du L, et al. (2006) Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proceedings of the National Academy of Sciences of the United States of America 103: 13578-13584.
16. Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, et al. (2004) Rise and fall of the Beringian steppe bison. Science 306: 1561-1565.
17. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A Draft Sequence of the Neandertal Genome. Science 328: 710-722.
18. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, et al. (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456: 387-390.
19. Reich D, Green RE, Kircher M, Krause J, Patterson N, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060.
20. Cooper A, Poinar HN, (2000) Ancient DNA: Do It Right or Not at All. Science 289: 1139.
21. Jurka J, (2000) Repbase Update- a database and an electronic journal of repetitive elements. Trends in Genetics 16: 418-420.