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Volumn 10, Issue 5, 2015, Pages 645-659

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; HYDROGEN SULFITE; SULFITE;

EID: 84929463154     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2015.039     Document Type: Article
Times cited : (150)

References (46)
  • 1
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21 (2002).
    • (2002) Genes Dev , vol.16 , pp. 6-21
    • Bird, A.1
  • 2
    • 84859910536 scopus 로고    scopus 로고
    • A unique regulatory phase of DNA methylation in the early mammalian embryo
    • Smith, Z.D. et al. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 484, 339-344 (2012).
    • (2012) Nature , vol.484 , pp. 339-344
    • Smith, Z.D.1
  • 3
    • 79960926264 scopus 로고    scopus 로고
    • Dynamic CpG island methylation landscape in oocytes and preimplantation embryos
    • Smallwood, S.A. et al. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat. Genet. 43, 811-814 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 811-814
    • Smallwood, S.A.1
  • 4
    • 80053348585 scopus 로고    scopus 로고
    • The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes
    • Gu, T.P. et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477, 606-610 (2011).
    • (2011) Nature , vol.477 , pp. 606-610
    • Gu, T.P.1
  • 5
    • 84872770694 scopus 로고    scopus 로고
    • Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine
    • Hackett, J.A. et al. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339, 448-452 (2013).
    • (2013) Science , vol.339 , pp. 448-452
    • Hackett, J.A.1
  • 6
    • 79952763586 scopus 로고    scopus 로고
    • Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine
    • Iqbal, K., Jin, S.G., Pfeifer, G.P. & Szabo, P.E. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl. Acad. Sci. USA 108, 3642-3647 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 3642-3647
    • Iqbal, K.1    Jin, S.G.2    Pfeifer, G.P.3    Szabo, P.E.4
  • 7
    • 0034598784 scopus 로고    scopus 로고
    • Demethylation of the zygotic paternal genome
    • Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature 403, 501-502 (2000).
    • (2000) Nature , vol.403 , pp. 501-502
    • Mayer, W.1    Niveleau, A.2    Walter, J.3    Fundele, R.4    Haaf, T.5
  • 8
    • 79952713567 scopus 로고    scopus 로고
    • 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming
    • Wossidlo, M. et al. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat. Commun. 2, 241 (2011).
    • (2011) Nat. Commun. , vol.2 , pp. 241
    • Wossidlo, M.1
  • 9
    • 75749142980 scopus 로고    scopus 로고
    • A role for the elongator complex in zygotic paternal genome demethylation
    • Okada, Y., Yamagata, K., Hong, K., Wakayama, T. & Zhang, Y. A role for the elongator complex in zygotic paternal genome demethylation. Nature 463, 554-558 (2010).
    • (2010) Nature , vol.463 , pp. 554-558
    • Okada, Y.1    Yamagata, K.2    Hong, K.3    Wakayama, T.4    Zhang, Y.5
  • 10
    • 84905030212 scopus 로고    scopus 로고
    • The DNA methylation landscape of human early embryos
    • Guo, H. et al. The DNA methylation landscape of human early embryos. Nature 511, 606-610 (2014).
    • (2014) Nature , vol.511 , pp. 606-610
    • Guo, H.1
  • 11
    • 84905052378 scopus 로고    scopus 로고
    • DNA methylation dynamics of the human preimplantation embryo
    • Smith, Z.D. et al. DNA methylation dynamics of the human preimplantation embryo. Nature 511, 611-615 (2014).
    • (2014) Nature , vol.511 , pp. 611-615
    • Smith, Z.D.1
  • 13
    • 84871702441 scopus 로고    scopus 로고
    • The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells
    • Seisenberger, S. et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 48, 849-862 (2012).
    • (2012) Mol. Cell , vol.48 , pp. 849-862
    • Seisenberger, S.1
  • 14
    • 84878282421 scopus 로고    scopus 로고
    • Epigenomic analysis of multilineage differentiation of human embryonic stem cells
    • Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134-1148 (2013).
    • (2013) Cell , vol.153 , pp. 1134-1148
    • Xie, W.1
  • 15
    • 84904962434 scopus 로고    scopus 로고
    • Epigenetics: Cellular memory erased in human embryos
    • Reik, W. & Kelsey, G. Epigenetics: cellular memory erased in human embryos. Nature 511, 540-541 (2014).
    • (2014) Nature , vol.511 , pp. 540-541
    • Reik, W.1    Kelsey, G.2
  • 16
    • 84906315296 scopus 로고    scopus 로고
    • Stem cells: Epigenome reprogramming-of mice and men
    • Burgess, D.J. Stem cells: epigenome reprogramming-of mice and men. Nat. Rev. Genet. 15, 571 (2014).
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 571
    • Burgess, D.J.1
  • 17
    • 84890526238 scopus 로고    scopus 로고
    • Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing
    • Guo, H. et al. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res. 23, 2126-2135 (2013).
    • (2013) Genome Res. , vol.23 , pp. 2126-2135
    • Guo, H.1
  • 18
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322 (2009).
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1
  • 19
    • 84876820776 scopus 로고    scopus 로고
    • Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases
    • Shirane, K. et al. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet. 9, e1003439 (2013).
    • (2013) PLoS Genet. , vol.9 , pp. e1003439
    • Shirane, K.1
  • 20
    • 80052937538 scopus 로고    scopus 로고
    • Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
    • Molaro, A. et al. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146, 1029-1041 (2011).
    • (2011) Cell , vol.146 , pp. 1029-1041
    • Molaro, A.1
  • 21
    • 84878292277 scopus 로고    scopus 로고
    • Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    • Gifford, C.A. et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153, 1149-1163 (2013).
    • (2013) Cell , vol.153 , pp. 1149-1163
    • Gifford, C.A.1
  • 22
    • 84882884517 scopus 로고    scopus 로고
    • Charting a dynamic DNA methylation landscape of the human genome
    • Ziller, M.J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-481 (2013).
    • (2013) Nature , vol.500 , pp. 477-481
    • Ziller, M.J.1
  • 23
    • 84879663784 scopus 로고    scopus 로고
    • Global epigenomic reconfiguration during mammalian brain development
    • Lister, R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905 (2013).
    • (2013) Science , vol.341 , pp. 1237905
    • Lister, R.1
  • 24
    • 84899091504 scopus 로고    scopus 로고
    • Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain
    • Wen, L. et al. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biol. 15, R49 (2014).
    • (2014) Genome Biol. , vol.15 , pp. R49
    • Wen, L.1
  • 25
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770 (2008).
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1
  • 26
    • 27144500218 scopus 로고    scopus 로고
    • Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
    • Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33, 5868-5877 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. 5868-5877
    • Meissner, A.1
  • 27
    • 79952788617 scopus 로고    scopus 로고
    • Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    • Gu, H. et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc. 6, 468-481 (2011).
    • (2011) Nat. Protoc. , vol.6 , pp. 468-481
    • Gu, H.1
  • 28
    • 84867539667 scopus 로고    scopus 로고
    • Genome-wide analysis of DNA methylation in low cell numbers by reduced representation bisulfite sequencing
    • Smallwood, S.A. & Kelsey, G. Genome-wide analysis of DNA methylation in low cell numbers by reduced representation bisulfite sequencing. Methods Mol. Biol. 925, 187-197 (2012).
    • (2012) Methods Mol. Biol. , vol.925 , pp. 187-197
    • Smallwood, S.A.1    Kelsey, G.2
  • 29
    • 67649854923 scopus 로고    scopus 로고
    • High-throughput bisulfite sequencing in mammalian genomes
    • Smith, Z.D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232 (2009).
    • (2009) Methods , vol.48 , pp. 226-232
    • Smith, Z.D.1    Gu, H.2    Bock, C.3    Gnirke, A.4    Meissner, A.5
  • 30
    • 77449153454 scopus 로고    scopus 로고
    • Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
    • Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods 7, 133-136 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 133-136
    • Gu, H.1
  • 31
    • 84866860120 scopus 로고    scopus 로고
    • Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling
    • Boyle, P. et al. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol. 13, R92 (2012).
    • (2012) Genome Biol. , vol.13 , pp. R92
    • Boyle, P.1
  • 32
    • 84905405443 scopus 로고    scopus 로고
    • Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
    • Smallwood, S.A. et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817-820 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 817-820
    • Smallwood, S.A.1
  • 33
    • 84866919003 scopus 로고    scopus 로고
    • Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    • Miura, F., Enomoto, Y., Dairiki, R. & Ito, T. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. 40, e136 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. e136
    • Miura, F.1    Enomoto, Y.2    Dairiki, R.3    Ito, T.4
  • 34
    • 84914817563 scopus 로고    scopus 로고
    • Active and passive demethylation of male and female pronuclear DNA in the mammalian zygote
    • Guo, F. et al. Active and passive demethylation of male and female pronuclear DNA in the mammalian zygote. Cell Stem Cell 15, 447-458 (2014).
    • (2014) Cell Stem Cell , vol.15 , pp. 447-458
    • Guo, F.1
  • 35
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for bisulfite-seq applications
    • Krueger, F. & Andrews, S.R. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27, 1571-1572 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 36
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: Whole-genome bisulfite sequence mapping program
    • Xi, Y. & Li, W. BSMAP: whole-genome bisulfite sequence mapping program. BMC Bioinformatics 10, 232 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 37
    • 77951125407 scopus 로고    scopus 로고
    • BS Seeker: Precise mapping for bisulfite sequencing
    • Chen, P.Y., Cokus, S.J. & Pellegrini, M. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11, 203 (2010).
    • (2010) BMC Bioinformatics , vol.11 , pp. 203
    • Chen, P.Y.1    Cokus, S.J.2    Pellegrini, M.3
  • 38
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 39
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 40
    • 77749323185 scopus 로고    scopus 로고
    • RNA-seq analysis to capture the transcriptome landscape of a single cell
    • Tang, F. et al. RNA-seq analysis to capture the transcriptome landscape of a single cell. Nat. Protoc. 5, 516-535 (2010).
    • (2010) Nat. Protoc. , vol.5 , pp. 516-535
    • Tang, F.1
  • 41
    • 67349146589 scopus 로고    scopus 로고
    • MRNA-seq whole-transcriptome analysis of a single cell
    • Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377-382 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 377-382
    • Tang, F.1
  • 42
    • 84883743509 scopus 로고    scopus 로고
    • Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells
    • Yan, L. et al. Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131-1139 (2013).
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 1131-1139
    • Yan, L.1
  • 43
    • 84868032982 scopus 로고    scopus 로고
    • Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain
    • Evrony, G.D. et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151, 483-496 (2012).
    • (2012) Cell , vol.151 , pp. 483-496
    • Evrony, G.D.1
  • 44
    • 40549127780 scopus 로고    scopus 로고
    • Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues
    • Frumkin, D. et al. Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues. BMC Biotechnol. 8, 17 (2008).
    • (2008) BMC Biotechnol. , vol.8 , pp. 17
    • Frumkin, D.1
  • 45
    • 79958122357 scopus 로고    scopus 로고
    • A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells
    • Ma, C. et al. A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells. Nat. Med. 17, 738-743 (2011).
    • (2011) Nat. Med. , vol.17 , pp. 738-743
    • Ma, C.1
  • 46
    • 78651304279 scopus 로고    scopus 로고
    • Whole-genome molecular haplotyping of single cells
    • Fan, H.C., Wang, J., Potanina, A. & Quake, S.R. Whole-genome molecular haplotyping of single cells. Nat. Biotechnol. 29, 51-57 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 51-57
    • Fan, H.C.1    Wang, J.2    Potanina, A.3    Quake, S.R.4


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