331
Views
0
CrossRef citations to date
0
Altmetric
Review

Epigenome sequencing comes of age in development, differentiation and disease mechanism research

&
Pages 207-220 | Published online: 20 Apr 2011

Bibliography

  • Eilertsen KJ , FloydZ,Gimble JM: The epigenetics of adult (somatic) stem cells. Crit. Rev. Eukaryot. Gene Expr.18(3) , 189–206 (2008).
  • Jones PA , BaylinSB: The epigenomics of cancer.Cell128(4) , 683–692 (2007).
  • Esteller M : Cancer epigenomics: DNA methylomes and histone-modification maps.Nat. Rev. Genet.8(4) , 286–298 (2007).
  • Jaenisch R ,Young R: Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell132(4) , 567–582 (2008).
  • Hanna J , CareyBW, JaenischR: Reprogramming of somatic cell identity.Cold Spring Harb. Symp. Quant. Biol.73 , 147–155 (2008).
  • Goldberg AD , AllisCD, BernsteinE: Epigenetics: a landscape takes shape.Cell128(4) , 635–638 (2007).
  • Bernstein BE , MeissnerA, LanderES: The mammalian epigenome.Cell128(4) , 669–681 (2007).
  • Bird A : Perceptions of epigenetics.Nature447(7143) , 396–398 (2007).
  • Barski A , CuddapahS, CuiKet al.: High-resolution profiling of histone methylations in the human genome.Cell129(4) , 823–837 (2007).
  • Wang Z , ZangC, RosenfeldJAet al.: Combinatorial patterns of histone acetylations and methylations in the human genome.Nat. Genet.40(7) , 897–903 (2008).
  • Taverna SD , LiH, RuthenburgAJ, AllisCD, PatelDJ: How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.Nat. Struct. Mol. Biol.14(11) , 1025–1040 (2007).
  • Ballestar E ,Wolffe AP: Methyl-CpG-binding proteins. Targeting specific gene repression. Eur. J. Biochem.268(1) , 1–6 (2001).
  • Dekker J : Gene regulation in the third dimension.Science319(5871) , 1793–1794 (2008).
  • Schoenfelder S , ClayI, FraserP: The transcriptional interactome: gene expression in 3D.Curr. Opin. Genet. Dev.20(2) , 127–133 (2010).
  • Shivaswamy S , BhingeA, ZhaoY, JonesS, HirstM, IyerVR: Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.PLoS Biol.6(3) , e65 (2008).
  • Schones DE , CuiK, CuddapahSet al.: Dynamic regulation of nucleosome positioning in the human genome.Cell132(5) , 887–898 (2008).
  • Mavrich TN , IoshikhesIP, VentersBJet al.: A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.Genome Res.18(7) , 1073–1083 (2008).
  • Yuan GC , LiuYJ, DionMFet al.: Genome-scale identification of nucleosome positions in S. cerevisiae.Science309(5734) , 626–630 (2005).
  • Ozsolak F , SongJS, LiuXS, FisherDE: High-throughput mapping of the chromatin structure of human promoters.Nat. Biotechnol.25(2) , 244–248 (2007).
  • Lee W , TilloD, BrayNet al.: A high-resolution atlas of nucleosome occupancy in yeast.Nat. Genet.39(10) , 1235–1244 (2007).
  • Sasaki S , MelloCC, ShimadaAet al.: Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.Science323(5912) , 401–404 (2009).
  • Kaplan N , MooreIK, Fondufe-MittendorfYet al.: The DNA-encoded nucleosome organization of a eukaryotic genome.Nature458(7236) , 362–366 (2009).
  • Valouev A , IchikawaJ, TonthatTet al.: A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.Genome Res.18(7) , 1051–1063 (2008).
  • Mikkelsen TS , KuM, JaffeDBet al.: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.Nature448(7153) , 553–560 (2007).
  • Bernstein BE , MikkelsenTS, XieXet al.: A bivalent chromatin structure marks key developmental genes in embryonic stem cells.Cell125(2) , 315–326 (2006).
  • Koch CM , AndrewsRM, FlicekPet al.: The landscape of histone modifications across 1% of the human genome in five human cell lines.Genome Res.17(6) , 691–707 (2007).
  • Bernstein BE , HumphreyEL, ErlichRLet al.: Methylation of histone H3 Lys 4 in coding regions of active genes.Proc. Natl Acad. Sci. USA99(13) , 8695–8700 (2002).
  • Robyr D , SukaY, XenariosIet al.: Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases.Cell109(4) , 437–446 (2002).
  • Schubeler D , MacalpineDM, ScalzoDet al.: The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.Genes Dev.18(11) , 1263–1271 (2004).
  • Liu CL , KaplanT, KimMet al.: Single-nucleosome mapping of histone modifications in S. cerevisiae.PLoS Biol.3(10) , e328 (2005).
  • Pokholok DK , HarbisonCT, LevineSet al.: Genome-wide map of nucleosome acetylation and methylation in yeast.Cell122(4) , 517–527 (2005).
  • Bernstein BE , KamalM, Lindblad-TohKet al.: Genomic maps and comparative analysis of histone modifications in human and mouse.Cell120(2) , 169–181 (2005).
  • Heintzman ND , StuartRK, HonGet al.: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.Nat. Genet.39(3) , 311–318 (2007).
  • Roh TY , NgauWC, CuiK, LandsmanD, ZhaoK: High-resolution genome-wide mapping of histone modifications.Nat. Biotechnol.22(8) , 1013–1016 (2004).
  • Guttman M , AmitI, GarberMet al.: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.Nature458(7235) , 223–227 (2009).
  • Yu H , ZhuS, ZhouB, XueH,Han JD: Inferring causal relationships among different histone modifications and gene expression. Genome Res.18(8) , 1314–1324 (2008).
  • Karlic R , ChungHR, LasserreJ, VlahovicekK, VingronM: Histone modification levels are predictive for gene expression.Proc. Natl Acad. Sci. USA107(7) , 2926–2931 (2010).
  • Bernstein BE , StamatoyannopoulosJA, CostelloJFet al.: The NIH Roadmap Epigenomics Mapping Consortium.Nat. Biotechnol.28(10) , 1045–1048 (2010).
  • He HH , MeyerCA, ShinHet al.: Nucleosome dynamics define transcriptional enhancers.Nat. Genet.42(4) , 343–347 (2010).
  • Cui K , ZangC, RohTYet al.: Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.Cell Stem Cell4(1) , 80–93 (2009).
  • Albert I , MavrichTN, TomshoLPet al.: Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.Nature446(7135) , 572–576 (2007).
  • Mavrich TN , JiangC, IoshikhesIPet al.: Nucleosome organization in the Drosophila genome.Nature453(7193) , 358–362 (2008).
  • Zhang Y , ShinH, SongJS, LeiY, LiuXS: Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.BMC Genomics9 , 537 (2008).
  • Schmid CD , BucherP: ChIP-Seq data reveal nucleosome architecture of human promoters.Cell131(5) , 831–832; author reply 832–833 (2007).
  • Laird PW : Principles and challenges of genome-wide DNA methylation analysis.Nat. Rev. Genet.11(3) , 191–203 (2010).
  • Brunner AL , JohnsonDS, KimSWet al.: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.Genome Res.19(6) , 1044–1056 (2009).
  • Ball MP , LiJB, GaoYet al.: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.Nat. Biotechnol.27(4) , 361–368 (2009).
  • Li J , GaoF, LiNet al.: An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.BMC Genomics10 , 223 (2009).
  • Jacinto FV , BallestarE, EstellerM: Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome.Biotechniques44(1) , 35, 37, 39 passim (2008).
  • Fouse SD , ShenY, PellegriniMet al.: Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation.Cell Stem Cell2(2) , 160–169 (2008).
  • Down TA , RakyanVK, TurnerDJet al.: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.Nat. Biotechnol.26(7) , 779–785 (2008).
  • Chavez L , JozefczukJ, GrimmCet al.: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.Genome Res.20(10) , 1441–1450 (2010).
  • Choy MK , MovassaghM, GohHG, BennettMR, DownTA, FooRS: Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated.BMC Genomics11 , 519 (2010).
  • Ruike Y , ImanakaY, SatoF, ShimizuK, TsujimotoG: Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing.BMC Genomics11 , 137 (2010).
  • Illingworth RS , Gruenewald-SchneiderU, WebbSet al.: Orphan CpG islands identify numerous conserved promoters in the mammalian genome.PLoS Genet.6(9) , e1001134 (2010).
  • Cokus SJ , FengS, ZhangXet al.: Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.Nature452(7184) , 215–219 (2008).
  • Lister R , O‘MalleyRC, Tonti-FilippiniJet al.: Highly integrated single-base resolution maps of the epigenome in Arabidopsis.Cell133(3) , 523–536 (2008).
  • Lister R , PelizzolaM, DowenRHet al.: Human DNA methylomes at base resolution show widespread epigenomic differences.Nature462(7271) , 315–322 (2009).
  • Xiang H , ZhuJ, ChenQet al.: Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.Nat. Biotechnol.28(5) , 516–520 (2010).
  • Popp C , DeanW, FengSet al.: Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.Nature463(7284) , 1101–1105 (2010).
  • Meissner A , GnirkeA, BellGW, RamsahoyeB, LanderES, JaenischR: Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.Nucleic Acids Res.33(18) , 5868–5877 (2005).
  • Meissner A , MikkelsenTS, GuHet al.: Genome-scale DNA methylation maps of pluripotent and differentiated cells.Nature454(7205) , 766–770 (2008).
  • Flusberg BA , WebsterDR, LeeJHet al.: Direct detection of DNA methylation during single-molecule, real-time sequencing.Nat. Methods7(6) , 461–465 (2010).
  • Clarke J , WuHC, JayasingheL, PatelA, ReidS, BayleyH: Continuous base identification for single-molecule nanopore DNA sequencing.Nat. Nanotechnol.4(4) , 265–270 (2009).
  • Li N , YeM, LiYet al.: Whole genome DNA methylation analysis based on high throughput sequencing technology.Methods (2010) (Epub ahead of print).
  • Robinson MD , StathamAL, SpeedTP, ClarkSJ: Protocol matters: which methylome are you actually studying?Epigenomics2(4) , 587–598 (2010).
  • Harris RA , WangT, CoarfaCet al.: Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.Nat. Biotechnol.28(10) , 1097–1105 (2010).
  • Bock C , TomazouEM, BrinkmanABet al.: Quantitative comparison of genome-wide DNA methylation mapping technologies.Nat. Biotechnol.28(10) , 1106–1114 (2010).
  • Serre D , LeeBH, TingAH: MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.Nucleic Acids Res.38(2) , 391–399 (2010).
  • Brinkman AB , SimmerF, MaK, KaanA, ZhuJ, StunnenbergHG: Whole-genome DNA methylation profiling using MethylCap-seq.Methods52(3) , 232–236 (2010).
  • Maunakea AK , NagarajanRP, BilenkyMet al.: Conserved role of intragenic DNA methylation in regulating alternative promoters.Nature466(7303) , 253–257 (2010).
  • Bibikova M , LeJ, BarnesBet al.: Genome-wide DNA methylation profiling using Infinium® assay.Epigenomics1(1) , 177–200 (2009).
  • Lieberman-Aiden E , Van Berkum NL, Williams L et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science326(5950) , 289–293 (2009).
  • Fullwood MJ , LiuMH, PanYFet al.: An oestrogen-receptor-alpha-bound human chromatin interactome.Nature462(7269) , 58–64 (2009).
  • Dekker J , RippeK, DekkerM, KlecknerN: Capturing chromosome conformation.Science295(5558) , 1306–1311 (2002).
  • Tanizawa H , IwasakiO, TanakaAet al.: Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation.Nucleic Acids Res.38(22) , 8164–8177 (2010).
  • Duan Z , AndronescuM, SchutzKet al.: A three-dimensional model of the yeast genome.Nature465(7296) , 363–367 (2010).
  • Harris EY , PontsN, LevchukA, RochKL, LonardiS: BRAT: bisulfite-treated reads analysis tool.Bioinformatics26(4) , 572–573 (2010).
  • Xi Y , LiW: BSMAP: whole genome bisulfite sequence MAPping program.BMC Bioinformatics10 , 232 (2009).
  • Chen PY , CokusSJ, PellegriniM: BS Seeker: precise mapping for bisulfite sequencing.BMC Bioinformatics11 , 203 (2010).
  • Zang C , SchonesDE, ZengC, CuiK, ZhaoK, PengW: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.Bioinformatics25(15) , 1952–1958 (2009).
  • Xu H , WeiCL, LinF, SungWK: An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.Bioinformatics24(20) , 2344–2349 (2008).
  • Hon G , RenB, WangW: ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.PLoS Comput. Biol.4(10) , e1000201 (2008).
  • Gu H , BockC, MikkelsenTSet al.: Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.Nat. Methods7(2) , 133–136 (2010).
  • Langmead B , TrapnellC, PopM, SalzbergSL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.Genome Biol.10(3) , R25 (2009).
  • Li H , DurbinR: Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics25(14) , 1754–1760 (2009).
  • Li H , DurbinR: Fast and accurate long-read alignment with Burrows-Wheeler transform.Bioinformatics26(5) , 589–595 (2010).
  • Li H , RuanJ, DurbinR: Mapping short DNA sequencing reads and calling variants using mapping quality scores.Genome Res.18(11) , 1851–1858 (2008).
  • Li R , YuC, LiYet al.: SOAP2: an improved ultrafast tool for short read alignment.Bioinformatics25(15) , 1966–1967 (2009).
  • Pepke S , WoldB, MortazaviA: Computation for ChIP-seq and RNA-seq studies.Nat. Methods6(11 Suppl) , S22–32 (2009).
  • Ji H , JiangH, MaW, JohnsonDS, MyersRM, WongWH: An integrated software system for analyzing ChIP-chip and ChIP-seq data.Nat. Biotechnol.26(11) , 1293–1300 (2008).
  • Johnson DS , MortazaviA, MyersRM, WoldB: Genome-wide mapping of in vivo protein-DNA interactions.Science316(5830) , 1497–1502 (2007).
  • Tuteja G , WhiteP, SchugJ, KaestnerKH: Extracting transcription factor targets from ChIP-Seq data.Nucleic Acids Res.37(17) , e113 (2009).
  • Zhang Y , LiuT, Meyer Ca et al.: Model-based analysis of ChIP-Seq (MACS). Genome Biol.9(9) , R137 (2008).
  • Rozowsky J , EuskirchenG, AuerbachRKet al.: PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.Nat. Biotechnol.27(1) , 66–75 (2009).
  • Valouev A , JohnsonDS, SundquistAet al.: Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.Nat. Methods5(9) , 829–834 (2008).
  • Jothi R , CuddapahS, BarskiA, CuiK, ZhaoK: Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.Nucleic Acids Res.36(16) , 5221–5231 (2008).
  • Kharchenko PV , TolstorukovMY, ParkPJ: Design and analysis of ChIP-seq experiments for DNA-binding proteins.Nat. Biotechnol.26(12) , 1351–1359 (2008).
  • Nix DA , CourdySJ, BoucherKM: Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.BMC Bioinformatics9 , 523 (2008).
  • Fejes AP , RobertsonG, BilenkyM, VarholR, BainbridgeM, JonesSJ: FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.Bioinformatics24(15) , 1729–1730 (2008).
  • Boyle AP , GuinneyJ, CrawfordGE, FureyTS: F-Seq: a feature density estimator for high-throughput sequence tags.Bioinformatics24(21) , 2537–2538 (2008).
  • Wilbanks EG , FacciottiMT: Evaluation of algorithm performance in ChIP-seq peak detection.PLoS One5(7) , e11471 (2010).
  • Munroe DJ , Harris Tjr: Third-generation sequencing fireworks at Marco Island. Nat. Biotech.28(5) , 426–428 (2010).

▪ Websites

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.