메뉴 건너뛰기




Volumn 10, Issue 5, 2015, Pages

Detection of cytosine methylation in ancient DNA from five native American populations using bisulfite sequencing

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; CYTOSINE; DNA; URACIL; RETROPOSON; SULFITE;

EID: 84959575426     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0125344     Document Type: Article
Times cited : (31)

References (45)
  • 1
    • 0036178007 scopus 로고    scopus 로고
    • DNA methylation and the regulation of gene transcription
    • PMID: 11915942
    • Attwood J, Yung RL, Richardson BC. DNA methylation and the regulation of gene transcription. Cell Mol. Life Sci. 2002; 59(2): 241-57. PMID: 11915942
    • (2002) Cell Mol. Life Sci , vol.59 , Issue.2 , pp. 241-257
    • Attwood, J.1    Yung, R.L.2    Richardson, B.C.3
  • 2
    • 34249279527 scopus 로고    scopus 로고
    • Stability and flexibility of epigenetic gene regulation in mammalian development
    • PMID: 17522676
    • Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007; 447(7143): 425-432. PMID: 17522676
    • (2007) Nature , vol.447 , Issue.7143 , pp. 425-432
    • Reik, W.1
  • 3
    • 0037372003 scopus 로고    scopus 로고
    • Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals
    • PMID: 12610534
    • Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 2003; 33: 245-254. PMID: 12610534
    • (2003) Nat. Genet , vol.33 , pp. 245-254
    • Jaenisch, R.1    Bird, A.2
  • 4
    • 77957970301 scopus 로고    scopus 로고
    • Epigenetic modifications and human disease
    • PMID: 20944598
    • Portela A, Esteller M. Epigenetic modifications and human disease. Nat. Biotechnol. 2010; 28(10): 1057-1068. doi: 10.1038/nbt.1685 PMID: 20944598
    • (2010) Nat. Biotechnol , vol.28 , Issue.10 , pp. 1057-1068
    • Portela, A.1    Esteller, M.2
  • 5
    • 0025299347 scopus 로고    scopus 로고
    • The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model
    • Sved J, Bird A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc. Natl. Acad. Sci. U.S.A. 2002; 87: 4692-6.
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.87 , pp. 4692-4696
    • Sved, J.1    Bird, A.2
  • 7
    • 0031638515 scopus 로고    scopus 로고
    • The host defense function of genomic methylation patterns
    • PMID: 9601018
    • Bestor T. The host defense function of genomic methylation patterns. Novartis Found. Symp. 1998; 214: 187-195. PMID: 9601018
    • (1998) Novartis Found. Symp , vol.214 , pp. 187-195
    • Bestor, T.1
  • 8
    • 77950862213 scopus 로고    scopus 로고
    • Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
    • PMID: 20026581
    • Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 2010; 38(6): 1-12. doi: 10.1093/nar/gkp1152 PMID: 20026581
    • (2010) Nucleic Acids Res , vol.38 , Issue.6 , pp. 1-12
    • Briggs, A.W.1    Stenzel, U.2    Meyer, M.3    Krause, J.4    Kircher, M.5    Pääbo, S.6
  • 9
    • 84900442346 scopus 로고    scopus 로고
    • Reconstructing the DNA methylation maps of the Neandertal and the Denisovan
    • PMID: 24786081
    • Gokhman D, Lavi E, Prufer K, Fraga MF, Riancho JA, Kelso J, et al. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science 2014; 344(6183): 523-527. doi: 10.1126/science.1250368 PMID: 24786081
    • (2014) Science , vol.344 , Issue.6183 , pp. 523-527
    • Gokhman, D.1    Lavi, E.2    Prufer, K.3    Fraga, M.F.4    Riancho, J.A.5    Kelso, J.6
  • 10
    • 84892911658 scopus 로고    scopus 로고
    • Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
    • PMID: 24299735
    • Pedersen J, Valen E, Velazquez AMV, Parker BJ, Rasmussen M, Lindgreen S, et al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 2014; 24: 454-466. doi: 10.1101/gr.163592.113 PMID: 24299735
    • (2014) Genome Res , vol.24 , pp. 454-466
    • Pedersen, J.1    Valen, E.2    Velazquez, A.M.V.3    Parker, B.J.4    Rasmussen, M.5    Lindgreen, S.6
  • 11
    • 84901583781 scopus 로고    scopus 로고
    • Deamination features of 5-hydroxymethylcytosine, a radical and enzymatic DNA oxidation product
    • Grand A, Jorge N, Morell C, Cadet J, Eriksson LA. Deamination features of 5-hydroxymethylcytosine, a radical and enzymatic DNA oxidation product. J Mol Model 2014; 20(2290): 1-10.
    • (2014) J Mol Model , vol.20 , Issue.2290 , pp. 1-10
    • Grand, A.1    Jorge, N.2    Morell, C.3    Cadet, J.4    Eriksson, L.A.5
  • 12
    • 84857891830 scopus 로고    scopus 로고
    • Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes
    • PMID: 22106369
    • Nestor C, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res. 2011; 22: 467-477. doi: 10.1101/gr.126417.111 PMID: 22106369
    • (2011) Genome Res , vol.22 , pp. 467-477
    • Nestor, C.1    Ottaviano, R.2    Reddington, J.3    Sproul, D.4    Reinhardt, D.5    Dunican, D.6
  • 13
    • 80052473600 scopus 로고    scopus 로고
    • Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development
    • PMID: 21747414
    • Rusov A, Tsenkina Y, Serio A, Dudnakova T, Fletcher J, Bai Y, et al. Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development. Cell Res. 2011; 21: 1332-1342. doi: 10.1038/cr.2011.113 PMID: 21747414
    • (2011) Cell Res , vol.21 , pp. 1332-1342
    • Rusov, A.1    Tsenkina, Y.2    Serio, A.3    Dudnakova, T.4    Fletcher, J.5    Bai, Y.6
  • 14
    • 0034687768 scopus 로고    scopus 로고
    • An unexpectedly high excision capacity for mispaired 5-hydroxymethyluracil in human cell extracts
    • PMID: 11121024
    • Rusmintratip V, Sowers L. An unexpectedly high excision capacity for mispaired 5-hydroxymethyluracil in human cell extracts. PNAS 2000; 97(26): 14183-14187. PMID: 11121024
    • (2000) PNAS , vol.97 , Issue.26 , pp. 14183-14187
    • Rusmintratip, V.1    Sowers, L.2
  • 16
    • 84904003161 scopus 로고    scopus 로고
    • Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process
    • PMID: 24993353
    • Smith O, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG, et al. Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci. Rep. 2014; 4(5559): 1-6. doi: 10.1038/srep05559 PMID: 24993353
    • (2014) Sci. Rep , vol.4 , Issue.5559 , pp. 1-6
    • Smith, O.1    Clapham, A.J.2    Rose, P.3    Liu, Y.4    Wang, J.5    Allaby, R.G.6
  • 17
    • 0030840954 scopus 로고    scopus 로고
    • Cytosine methylation and the ecology of intragenomic parasites
    • PMID: 9260521
    • Yoder J, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997; 13(8): 335-340. PMID: 9260521
    • (1997) Trends Genet , vol.13 , Issue.8 , pp. 335-340
    • Yoder, J.1    Walsh, C.P.2    Bestor, T.H.3
  • 18
    • 17344370076 scopus 로고    scopus 로고
    • The impact of L1 retrotransposons on the human genome
    • PMID: 9590283
    • Kazazian H, Moran J. The impact of L1 retrotransposons on the human genome. Nat. Genet. 1998; 19(1): 19-24. PMID: 9590283
    • (1998) Nat. Genet , vol.19 , Issue.1 , pp. 19-24
    • Kazazian, H.1    Moran, J.2
  • 19
    • 0034086210 scopus 로고    scopus 로고
    • L1 (LINE-1) retrotransposon evolution and amplification in recent human history
    • PMID: 10833198
    • Boissinot S, Chevret P, Furano AV. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 2000; 17: 915-928. PMID: 10833198
    • (2000) Mol. Biol. Evol , vol.17 , pp. 915-928
    • Boissinot, S.1    Chevret, P.2    Furano, A.V.3
  • 20
    • 0033786249 scopus 로고    scopus 로고
    • Reading between the LINEs: Human genomic variation induced by LINE-1 retrotransposition
    • PMID: 11042149
    • Sheen F, Sherry ST, Risch GM, Robichaux M, Nasidze I, Stoneking M, et al. Reading between the LINEs: Human genomic variation induced by LINE-1 retrotransposition. Genome Res. 2000; 10(10): 1496-1508. PMID: 11042149
    • (2000) Genome Res , vol.10 , Issue.10 , pp. 1496-1508
    • Sheen, F.1    Sherry, S.T.2    Risch, G.M.3    Robichaux, M.4    Nasidze, I.5    Stoneking, M.6
  • 23
    • 36749066742 scopus 로고    scopus 로고
    • Migration and social structure among the Hopewell: Evidence from ancient DNA
    • Bolnick D, Smith D. Migration and social structure among the Hopewell: Evidence from ancient DNA. Am Antiq 2007; 72(4): 627-644.
    • (2007) Am Antiq , vol.72 , Issue.4 , pp. 627-644
    • Bolnick, D.1    Smith, D.2
  • 24
    • 84869489174 scopus 로고    scopus 로고
    • The genetic impact of Aztec imperialism: Ancient mitochondrial DNA evidence from Xaltocan, Mexico
    • PMID: 23076995
    • Mata-Míguez J, Overholtzer L, Rodríguez-Alegría E, Kemp BM, Bolnick D. The genetic impact of Aztec imperialism: Ancient mitochondrial DNA evidence from Xaltocan, Mexico. Am. J. Phys. Anth. 2012; 149(4): 504-516. doi: 10.1002/ajpa.22152 PMID: 23076995
    • (2012) Am. J. Phys. Anth , vol.149 , Issue.4 , pp. 504-516
    • Mata-Míguez, J.1    Overholtzer, L.2    Rodríguez-Alegría, E.3    Kemp, B.M.4    Bolnick, D.5
  • 25
    • 84880562365 scopus 로고    scopus 로고
    • Brief communication: Evolution of a specific o allele (o1v(g542a)) supports unique ancestry of native americans
    • PMID: 23868176
    • Villanea F, Bolnick D, Monroe C, Worl R, Cambra R, Leventhal A, et al. Brief communication: Evolution of a specific O allele (O1v(G542A)) supports unique ancestry of Native Americans. Am. J. Phys. Anthropol. 2013; 151(4): 649-657. doi: 10.1002/ajpa.22292 PMID: 23868176
    • (2013) Am. J. Phys. Anthropol , vol.151 , Issue.4 , pp. 649-657
    • Villanea, F.1    Bolnick, D.2    Monroe, C.3    Worl, R.4    Cambra, R.5    Leventhal, A.6
  • 26
    • 34548579114 scopus 로고    scopus 로고
    • Ancient DNA extraction from bones and teeth
    • Rohland N, Hofreiter M. Ancient DNA extraction from bones and teeth. Nat. Prot. 2007; 2: 1756-1762.
    • (2007) Nat. Prot , vol.2 , pp. 1756-1762
    • Rohland, N.1    Hofreiter, M.2
  • 27
    • 0036998955 scopus 로고    scopus 로고
    • ABO blood group genotyping of ancient DNA by PCRRFLP
    • PMID: 12461639
    • Hummel S, Schmidt D, Kahle M, Hermann B. ABO blood group genotyping of ancient DNA by PCRRFLP. Int. J. Legal Med. 2002; 116: 327-333. PMID: 12461639
    • (2002) Int. J. Legal Med , vol.116 , pp. 327-333
    • Hummel, S.1    Schmidt, D.2    Kahle, M.3    Hermann, B.4
  • 28
    • 33748741378 scopus 로고    scopus 로고
    • Repeat silica extraction: A simple technique for the removal of PCR inhibitors from DNA extracts
    • Kemp BM, Monroe C, Smith DG. Repeat silica extraction: A simple technique for the removal of PCR inhibitors from DNA extracts. J Arch. Sci. 2006; 33: 1680-1689.
    • (2006) J Arch. Sci , vol.33 , pp. 1680-1689
    • Kemp, B.M.1    Monroe, C.2    Smith, D.G.3
  • 29
    • 77649188745 scopus 로고    scopus 로고
    • A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts
    • PMID: 20041847
    • King C, Debruyne R, Kuch M, Schwarz C, Poinar H. A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts. BioTechniques 2009; 47: 941-9. doi: 10.2144/000113244 PMID: 20041847
    • (2009) BioTechniques , vol.47 , pp. 941-949
    • King, C.1    Debruyne, R.2    Kuch, M.3    Schwarz, C.4    Poinar, H.5
  • 30
    • 67249110285 scopus 로고    scopus 로고
    • New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains
    • PMID: 19321502
    • Schwarz C, Debruyne R, Kuch M, McNally E, Schwarcz H, Aubrey AD, et al. New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nuc. Ac. Res. 2009; 37: 3215-3229. doi: 10.1093/nar/gkp159 PMID: 19321502
    • (2009) Nuc. Ac. Res , vol.37 , pp. 3215-3229
    • Schwarz, C.1    Debruyne, R.2    Kuch, M.3    McNally, E.4    Schwarcz, H.5    Aubrey, A.D.6
  • 32
    • 0040074358 scopus 로고    scopus 로고
    • Ancient DNA in Anthropology: Methods, applications, and ethics
    • Kaestle F, Horsburgh K. Ancient DNA in Anthropology: methods, applications, and ethics. Yearb. Phys. Anthropol. 2002; 45: 92-130.
    • (2002) Yearb. Phys. Anthropol , vol.45 , pp. 92-130
    • Kaestle, F.1    Horsburgh, K.2
  • 36
    • 84863304598 scopus 로고    scopus 로고
    • A language and environment for statistical computing
    • Vienna, Austria. PMID: 23519455
    • R Core Team. A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. 2013. doi: 10.3758/s13428-013-0330-5 PMID: 23519455
    • (2013) R Foundation for Statistical Computing
  • 37
    • 0035407651 scopus 로고    scopus 로고
    • Bisulfite genomic sequencing: Systematic investigation of critical experimental parameters
    • Grunau C, Clark SJ, Rosenthal A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res. 2001; 29(13): 1-7.
    • (2001) Nucleic Acids Res , vol.29 , Issue.13 , pp. 1-7
    • Grunau, C.1    Clark, S.J.2    Rosenthal, A.3
  • 38
    • 0033064929 scopus 로고    scopus 로고
    • DNA preservation: A microsatellite-DNA study on ancient skeletal remains
    • PMID: 10435438
    • Burger J, Hummel S, Hermann B, Henke W. DNA preservation: A microsatellite-DNA study on ancient skeletal remains. Electrophoresis 1999; 20: 1722-1728. PMID: 10435438
    • (1999) Electrophoresis , vol.20 , pp. 1722-1728
    • Burger, J.1    Hummel, S.2    Hermann, B.3    Henke, W.4
  • 39
    • 79952187261 scopus 로고    scopus 로고
    • Survival and recovery of DNA from ancient teeth and bones
    • Adler CJ, Haak W, Donlon D, Cooper A. Survival and recovery of DNA from ancient teeth and bones. J. Archaeol. Sci. 2011; 38: 956-964.
    • (2011) J. Archaeol. Sci , vol.38 , pp. 956-964
    • Adler, C.J.1    Haak, W.2    Donlon, D.3    Cooper, A.4
  • 40
    • 84868087346 scopus 로고    scopus 로고
    • The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils
    • PMID: 23055061
    • Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. B. 2012; 279(1748): 4724-4733. doi: 10.1098/rspb. 2012.1745 PMID: 23055061
    • (2012) Proc. B , vol.279 , Issue.1748 , pp. 4724-4733
    • Allentoft, M.E.1    Collins, M.2    Harker, D.3    Haile, J.4    Oskam, C.L.5    Hale, M.L.6
  • 41
    • 84855512692 scopus 로고    scopus 로고
    • DNA in ancient bone-Where is it located and how should we extract it?
    • PMID: 21855309
    • Campos P, Craig OE, Turner-Walker G, Peacock E, Willerslev E, Gilbert MTP. DNA in ancient bone-Where is it located and how should we extract it? Ann. Anat. 2012; 194: 7-16. doi: 10.1016/j.aanat. 2011.07.003 PMID: 21855309
    • (2012) Ann. Anat , vol.194 , pp. 7-16
    • Campos, P.1    Craig, O.E.2    Turner-Walker, G.3    Peacock, E.4    Willerslev, E.5    Gilbert, M.T.P.6
  • 42
    • 79958186419 scopus 로고    scopus 로고
    • Dietary patterns are associated with levels of global genomic DNA methylation in a cancer-free population
    • PMID: 21525250
    • Zhang F, Morabia A, Carroll J, Gonzalez K, Fulda K, Kaur M, et al. Dietary patterns are associated with levels of global genomic DNA methylation in a cancer-free population. J. Nutr. 2011; 141(6): 1165-1171. doi: 10.3945/jn.110.134536 PMID: 21525250
    • (2011) J. Nutr , vol.141 , Issue.6 , pp. 1165-1171
    • Zhang, F.1    Morabia, A.2    Carroll, J.3    Gonzalez, K.4    Fulda, K.5    Kaur, M.6
  • 44
    • 84859112401 scopus 로고    scopus 로고
    • Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA
    • Sawyer S, Krause J, Guschanski K, Savolainen C, Paabo S. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One 2012; 7(3): 1-7.
    • (2012) PLoS One , vol.7 , Issue.3 , pp. 1-7
    • Sawyer, S.1    Krause, J.2    Guschanski, K.3    Savolainen, C.4    Paabo, S.5
  • 45
    • 84905901789 scopus 로고    scopus 로고
    • An epigenetic window into the past?
    • PMID: 25082684
    • Orlando L, Willerslev E. An epigenetic window into the past? Science 2014; 345(6196): 511-512. doi: 10.1126/science.1256515 PMID: 25082684
    • (2014) Science , vol.345 , Issue.6196 , pp. 511-512
    • Orlando, L.1    Willerslev, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.