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Volumn 2, Issue 2, 2010, Pages 187-197

Analysis of the primary structure of chromatin with next-generation sequencing

Author keywords

chromatin; histone modifications; next generation sequencing; nucleosome positioning

Indexed keywords

DNA; HISTONE;

EID: 77954097433     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.09.48     Document Type: Review
Times cited : (10)

References (72)
  • 1
    • 0033529565 scopus 로고    scopus 로고
    • Twenty-fve years of the nucleosome, fundamental particle of the eukaryote chromosome
    • Kornberg RD, Lorch Y: Twenty-fve years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98(3), 285-294 (1999).
    • (1999) Cell , vol.98 , Issue.3 , pp. 285-294
    • Kornberg, R.D.1    Lorch, Y.2
  • 2
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389(6648), 251-260 (1997).
    • (1997) Nature , vol.389 , Issue.6648 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 3
    • 0030812908 scopus 로고    scopus 로고
    • Transcription factor access to chromatin
    • Beato M, Eisfeld K: Transcription factor access to chromatin. Nucleic Acids Res. 25(18), 3559-3563 (1997).
    • (1997) Nucleic Acids Res , vol.25 , Issue.18 , pp. 3559-3563
    • Beato, M.1    Eisfeld, K.2
  • 4
    • 0033119021 scopus 로고    scopus 로고
    • Chromatin-modifying and-remodeling complexes
    • Kornberg RD, Lorch Y: Chromatin-modifying and-remodeling complexes. Curr. Opin. Genet. Dev. 9(2), 148-151 (1999).
    • (1999) Curr. Opin. Genet. Dev , vol.9 , Issue.2 , pp. 148-151
    • Kornberg, R.D.1    Lorch, Y.2
  • 5
    • 0035839136 scopus 로고    scopus 로고
    • Translating the histone code
    • Jenuwein T, Allis CD: Translating the histone code. Science 293(5532), 1074-1080 (2001).
    • (2001) Science , vol.293 , Issue.5532 , pp. 1074-1080
    • Jenuwein, T.1    Allis, C.D.2
  • 7
    • 0023948705 scopus 로고
    • Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
    • Solomon MJ, Larsen PL, Varshavsky A: Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53(6), 937-947 (1988).
    • (1988) Cell , vol.53 , Issue.6 , pp. 937-947
    • Solomon, M.J.1    Larsen, P.L.2    Varshavsky, A.3
  • 8
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD: Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36(8), 900-905 (2004).
    • (2004) Nat. Genet , vol.36 , Issue.8 , pp. 900-905
    • Lee, C.K.1    Shibata, Y.2    Rao, B.3    Strahl, B.D.4    Lieb, J.D.5
  • 9
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identifcation of nucleosome positions in S. cerevisiae
    • Yuan GC, Liu YJ, Dion MF et al.: Genome-scale identifcation of nucleosome positions in S. cerevisiae. Science 309(5734), 626-630 (2005).
    • (2005) Science , vol.309 , Issue.5734 , pp. 626-630
    • Yuan, G.C.1    Liu, Y.J.2    Dion, M.F.3
  • 10
    • 33846862405 scopus 로고    scopus 로고
    • High-throughput mapping of the chromatin structure of human promoters
    • Ozsolak F, Song JS, Liu XS, Fisher DE: High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol. 25(2), 244-248 (2007).
    • (2007) Nat. Biotechnol , vol.25 , Issue.2 , pp. 244-248
    • Ozsolak, F.1    Song, J.S.2    Liu, X.S.3    Fisher, D.E.4
  • 11
    • 34748826166 scopus 로고    scopus 로고
    • A high-resolution atlas of nucleosome occupancy in yeast
    • Lee W, Tillo D, Bray N et al.: A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 39(10), 1235-1244 (2007).
    • (2007) Nat. Genet , vol.39 , Issue.10 , pp. 1235-1244
    • Lee, W.1    Tillo, D.2    Bray, N.3
  • 12
    • 43749099875 scopus 로고    scopus 로고
    • Nucleosome organization in the Drosophila genome
    • Mavrich TN, Jiang C, Ioshikhes IP et al.: Nucleosome organization in the Drosophila genome. Nature 453(7193), 358-362 (2008).
    • (2008) Nature , vol.453 , Issue.7193 , pp. 358-362
    • Mavrich, T.N.1    Jiang, C.2    Ioshikhes, I.P.3
  • 13
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • Bentley DR: Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16(6), 545-552 (2006).
    • (2006) Curr. Opin. Genet. Dev , vol.16 , Issue.6 , pp. 545-552
    • Bentley, D.R.1
  • 14
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure J, Ji H: Next-generation DNA sequencing. Nat. Biotechnol. 26(10), 1135-1145 (2008).
    • (2008) Nat. Biotechnol , vol.26 , Issue.10 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 15
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis ER: Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387-402 (2008).
    • (2008) Annu. Rev. Genomics Hum. Genet , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 16
    • 33845298285 scopus 로고    scopus 로고
    • Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
    • Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ: Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 16(12), 1505-1516 (2006).
    • (2006) Genome Res , vol.16 , Issue.12 , pp. 1505-1516
    • Johnson, S.M.1    Tan, F.J.2    McCullough, H.L.3    Riordan, D.P.4    Fire, A.Z.5
  • 17
    • 46449103738 scopus 로고    scopus 로고
    • A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
    • Valouev A, Ichikawa J, Tonthat T et 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).
    • (2008) Genome Res , vol.18 , Issue.7 , pp. 1051-1063
    • Valouev, A.1    Ichikawa, J.2    Tonthat, T.3
  • 18
    • 57149119464 scopus 로고    scopus 로고
    • Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    • Field Y, Kaplan N, Fondufe-Mittendorf Y et al.: Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 4(11), E1000216 (2008).
    • (2008) PLoS Comput. Biol , vol.4 , Issue.11
    • Field, Y.1    Kaplan, N.2    Fondufe-Mittendorf, Y.3
  • 19
    • 63449135035 scopus 로고    scopus 로고
    • Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
    • Field Y, Fondufe-Mittendorf Y, Moore IK et al.: Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat. Genet. 41(4), 438-445 (2009).
    • (2009) Nat. Genet , vol.41 , Issue.4 , pp. 438-445
    • Field, Y.1    Fondufe-Mittendorf, Y.2    Moore, I.K.3
  • 20
    • 62649085538 scopus 로고    scopus 로고
    • The DNA-encoded nucleosome organization of a eukaryotic genome
    • Kaplan N, Moore IK, Fondufe-Mittendorf Y et al.: The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458(7236), 362-366 (2009).
    • (2009) Nature , vol.458 , Issue.7236 , pp. 362-366
    • Kaplan, N.1    Moore, I.K.2    Fondufe-Mittendorf, Y.3
  • 21
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • Schones DE, Cui K, Cuddapah S et al.: Dynamic regulation of nucleosome positioning in the human genome. Cell 132(5), 887-898 (2008).
    • (2008) Cell , vol.132 , Issue.5 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3
  • 22
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • Albert I, Mavrich TN, Tomsho LP et al.: Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446(7135), 572-576 (2007).
    • (2007) Nature , vol.446 , Issue.7135 , pp. 572-576
    • Albert, I.1    Mavrich, T.N.2    Tomsho, L.P.3
  • 23
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profling of histone methylations in the human genome
    • Barski A, Cuddapah S, Cui K et al.: High-resolution profling of histone methylations in the human genome. Cell 129(4), 823-837 (2007).
    • (2007) Cell , vol.129 , Issue.4 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3
  • 24
    • 46249112085 scopus 로고    scopus 로고
    • Combinatorial patterns of histone acetylations and methylations in the human genome
    • Wang Z, Zang C, Rosenfeld JA et al.: Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40(7), 897-903 (2008).
    • (2008) Nat. Genet , vol.40 , Issue.7 , pp. 897-903
    • Wang, Z.1    Zang, C.2    Rosenfeld, J.A.3
  • 25
    • 68149150830 scopus 로고    scopus 로고
    • H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
    • Jin C, Zang C, Wei G et al.: H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat. Genet. 41(8), 941-945 (2009).
    • (2009) Nat. Genet , vol.41 , Issue.8 , pp. 941-945
    • Jin, C.1    Zang, C.2    Wei, G.3
  • 26
    • 57149096220 scopus 로고    scopus 로고
    • Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding
    • Robertson AG, Bilenky M, Tam A et al.: Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. Genome Res. 18(12), 1906-1917 (2008).
    • (2008) Genome Res , vol.18 , Issue.12 , pp. 1906-1917
    • Robertson, A.G.1    Bilenky, M.2    Tam, A.3
  • 27
    • 41749091787 scopus 로고    scopus 로고
    • Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
    • Shivaswamy S, Bhinge A, Zhao Y et al.: Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 6(3), E65 (2008).
    • (2008) PLoS Biol , vol.6 , Issue.3
    • Shivaswamy, S.1    Bhinge, A.2    Zhao, Y.3
  • 28
    • 67349261087 scopus 로고    scopus 로고
    • High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA
    • Fraser RM, Keszenman-Pereyra D, Simmen MW, Allan J: High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA. J. Mol. Biol. 390(2), 292-305 (2009).
    • (2009) J. Mol. Biol , vol.390 , Issue.2 , pp. 292-305
    • Fraser, R.M.1    Keszenman-Pereyra, D.2    Simmen, M.W.3    Allan, J.4
  • 29
    • 57449095143 scopus 로고    scopus 로고
    • Identifying positioned nucleosomes with epigenetic marks in human from ChIP-seq
    • Zhang Y, Shin H, Song JS, Lei Y, Liu XS: Identifying positioned nucleosomes with epigenetic marks in human from ChIP-seq. BMC Genomics 9, 537 (2008).
    • (2008) BMC Genomics , vol.9 , pp. 537
    • Zhang, Y.1    Shin, H.2    Song, J.S.3    Lei, Y.4    Liu, X.S.5
  • 30
    • 66449128244 scopus 로고    scopus 로고
    • Comparative ana lysis of H2A.Z nucleosome organization in the human and yeast genomes
    • Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ: Comparative ana lysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 19(6), 967-977 (2009).
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 967-977
    • Tolstorukov, M.Y.1    Kharchenko, P.V.2    Goldman, J.A.3    Kingston, R.E.4    Park, P.J.5
  • 31
    • 48249153426 scopus 로고    scopus 로고
    • The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome
    • Fu Y, Sinha M, Peterson CL, Weng Z: The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4(7), E1000138 (2008).
    • (2008) PLoS Genet , vol.4 , Issue.7
    • Fu, Y.1    Sinha, M.2    Peterson, C.L.3    Weng, Z.4
  • 32
    • 69849085802 scopus 로고    scopus 로고
    • Genome-wide maps of mono-and di-nucleosomes of Aspergillus fumigatus
    • Nishida H, Motoyama T, Yamamoto S, Aburatani H, Osada H: Genome-wide maps of mono-and di-nucleosomes of Aspergillus fumigatus. Bio informatics 25(18), 2295-2297 (2009).
    • (2009) Bio Informatics , vol.25 , Issue.18 , pp. 2295-2297
    • Nishida, H.1    Motoyama, T.2    Yamamoto, S.3    Aburatani, H.4    Osada, H.5
  • 33
    • 34548267126 scopus 로고    scopus 로고
    • Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells
    • Dalal Y, Wang H, Lindsay S, Henikoff S: Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol. 5(8), E218 (2007).
    • (2007) PLoS Biol , vol.5 , Issue.8
    • Dalal, Y.1    Wang, H.2    Lindsay, S.3    Henikoff, S.4
  • 34
    • 4444312848 scopus 로고    scopus 로고
    • Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA
    • Bao Y, Konesky K, Park YJ et al.: Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. EMBO J. 23(16), 3314-3324 (2004).
    • (2004) EMBO J , vol.23 , Issue.16 , pp. 3314-3324
    • Bao, Y.1    Konesky, K.2    Park, Y.J.3
  • 35
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: Advances through genomics
    • Jiang C, Pugh BF: Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10(3), 161-172 (2009).
    • (2009) Nat. Rev. Genet , vol.10 , Issue.3 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 36
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifcations
    • Schones DE, Zhao K: Genome-wide approaches to studying chromatin modifcations. Nat. Rev. Genet. 9(3), 179-191 (2008).
    • (2008) Nat. Rev. Genet , vol.9 , Issue.3 , pp. 179-191
    • Schones, D.E.1    Zhao, K.2
  • 37
    • 67649826220 scopus 로고    scopus 로고
    • From DNA sequence to transcriptional behaviour: A quantitative approach
    • Segal E, Widom J: From DNA sequence to transcriptional behaviour: a quantitative approach. Nat. Rev. Genet. 10(7), 443-456 (2009).
    • (2009) Nat. Rev. Genet , vol.10 , Issue.7 , pp. 443-456
    • Segal, E.1    Widom, J.2
  • 38
    • 33947303168 scopus 로고    scopus 로고
    • Transposable elements and the epigenetic regulation of the genome
    • Slotkin RK, Martienssen R: Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8(4), 272-285 (2007).
    • (2007) Nat. Rev. Genet , vol.8 , Issue.4 , pp. 272-285
    • Slotkin, R.K.1    Martienssen, R.2
  • 39
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • Heintzman ND, Stuart RK, Hon G et al.: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39(3), 311-318 (2007).
    • (2007) Nat. Genet , vol.39 , Issue.3 , pp. 311-318
    • Heintzman, N.D.1    Stuart, R.K.2    Hon, G.3
  • 40
    • 55549118625 scopus 로고    scopus 로고
    • ChromaSig: A probabilistic approach to fnding common chromatin signatures in the human genome
    • Hon G, Ren B, Wang W: ChromaSig: a probabilistic approach to fnding common chromatin signatures in the human genome. PLoS Comput. Biol. 4(10), E1000201 (2008).
    • (2008) PLoS Comput. Biol , vol.4 , Issue.10
    • Hon, G.1    Ren, B.2    Wang, W.3
  • 41
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissue-specifc activity of enhancers
    • Visel A, Blow MJ, Li Z et al.: ChIP-seq accurately predicts tissue-specifc activity of enhancers. Nature 457(7231), 854-858 (2009).
    • (2009) Nature , vol.457 , Issue.7231 , pp. 854-858
    • Visel, A.1    Blow, M.J.2    Li, Z.3
  • 42
    • 33747500567 scopus 로고    scopus 로고
    • A genomic code for nucleosome positioning
    • Segal E, Fondufe-Mittendorf Y, Chen L et al.: A genomic code for nucleosome positioning. Nature 442(7104), 772-778 (2006).
    • (2006) Nature , vol.442 , Issue.7104 , pp. 772-778
    • Segal, E.1    Fondufe-Mittendorf, Y.2    Chen, L.3
  • 43
    • 34547643563 scopus 로고    scopus 로고
    • Nucleosome positioning signals in genomic DNA
    • Peckham HE, Thurman RE, Fu Y et al.: Nucleosome positioning signals in genomic DNA. Genome Res. 17(8), 1170-1177 (2007).
    • (2007) Genome Res , vol.17 , Issue.8 , pp. 1170-1177
    • Peckham, H.E.1    Thurman, R.E.2    Fu, Y.3
  • 44
    • 46449112319 scopus 로고    scopus 로고
    • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    • Mavrich TN, Ioshikhes IP, Venters BJ et al.: A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18(7), 1073-1083 (2008).
    • (2008) Genome Res , vol.18 , Issue.7 , pp. 1073-1083
    • Mavrich, T.N.1    Ioshikhes, I.P.2    Venters, B.J.3
  • 45
  • 46
    • 68249142923 scopus 로고    scopus 로고
    • Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
    • Zhang Y, Moqtaderi Z, Rattner BP et al.: Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat. Struct. Mol. Biol. 16(8), 847-852 (2009).
    • (2009) Nat. Struct. Mol. Biol , vol.16 , Issue.8 , pp. 847-852
    • Zhang, Y.1    Moqtaderi, Z.2    Rattner, B.P.3
  • 47
    • 60849083224 scopus 로고    scopus 로고
    • Sequence-dependent nucleosome positioning
    • Chung HR, Vingron M: Sequence-dependent nucleosome positioning. J. Mol. Biol. 386(5), 1411-1422 (2009).
    • (2009) J. Mol. Biol , vol.386 , Issue.5 , pp. 1411-1422
    • Chung, H.R.1    Vingron, M.2
  • 48
    • 0001415964 scopus 로고
    • The pitch of chromatin DNA is refected in its nucleotide sequence
    • Trifonov EN, Sussman JL: The pitch of chromatin DNA is refected in its nucleotide sequence. Proc. Natl Acad. Sci. USA 77(7), 3816-3820 (1980).
    • (1980) Proc. Natl Acad. Sci. USA , vol.77 , Issue.7 , pp. 3816-3820
    • Trifonov, E.N.1    Sussman, J.L.2
  • 50
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell SC, Drew HR, Travers AA: Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191(4), 659-675 (1986).
    • (1986) J. Mol. Biol , vol.191 , Issue.4 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Travers, A.A.3
  • 51
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:dT) tracts: Major determinants of nucleosome organization
    • Segal E, Widom J: Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr. Opin. Struct. Biol. 19(1), 65-71 (2009).
    • (2009) Curr. Opin. Struct. Biol , vol.19 , Issue.1 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 52
    • 0024261880 scopus 로고
    • Statistical positioning of nucleosomes by specifc protein-binding to an upstream activating sequence in yeast
    • Fedor MJ, Lue NF, Kornberg RD: Statistical positioning of nucleosomes by specifc protein-binding to an upstream activating sequence in yeast. J. Mol. Biol. 204(1), 109-127 (1988).
    • (1988) J. Mol. Biol , vol.204 , Issue.1 , pp. 109-127
    • Fedor, M.J.1    Lue, N.F.2    Kornberg, R.D.3
  • 53
    • 34250168295 scopus 로고    scopus 로고
    • Rules and regulation in the primary structure of chromatin
    • Rando OJ, Ahmad K: Rules and regulation in the primary structure of chromatin. Curr. Opin. Cell Biol. 19(3), 250-256 (2007).
    • (2007) Curr. Opin. Cell Biol , vol.19 , Issue.3 , pp. 250-256
    • Rando, O.J.1    Ahmad, K.2
  • 54
    • 0035997356 scopus 로고    scopus 로고
    • ATP-dependent nucleosome remodeling
    • Becker PB, Horz W: ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247-273 (2002).
    • (2002) Annu. Rev. Biochem , vol.71 , pp. 247-273
    • Becker, P.B.1    Horz, W.2
  • 55
    • 38949204996 scopus 로고    scopus 로고
    • Genomic sequence is highly predictive of local nucleosome depletion
    • Yuan GC, Liu JS: Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput. Biol. 4(1), E13 (2008).
    • (2008) PLoS Comput. Biol , vol.4 , Issue.1
    • Yuan, G.C.1    Liu, J.S.2
  • 56
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke A, Melnikov A, Maguire J et al.: Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27(2), 182-189 (2009).
    • (2009) Nat. Biotechnol , vol.27 , Issue.2 , pp. 182-189
    • Gnirke, A.1    Melnikov, A.2    Maguire, J.3
  • 57
    • 67649631522 scopus 로고    scopus 로고
    • Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection
    • Herman DS, Hovingh GK, Iartchouk O et al.: Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection. Nat. Methods 6(7), 507-510 (2009).
    • (2009) Nat. Methods , vol.6 , Issue.7 , pp. 507-510
    • Herman, D.S.1    Hovingh, G.K.2    Iartchouk, O.3
  • 58
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park PJ: ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet. 10(10), 669-680 (2009).
    • (2009) Nat. Rev. Genet , vol.10 , Issue.10 , pp. 669-680
    • Park, P.J.1
  • 59
    • 61849170193 scopus 로고    scopus 로고
    • Genome-wide profling of salt fractions maps physical properties of chromatin
    • Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K: Genome-wide profling of salt fractions maps physical properties of chromatin. Genome Res. 19(3), 460-469 (2009).
    • (2009) Genome Res , vol.19 , Issue.3 , pp. 460-469
    • Henikoff, S.1    Henikoff, J.G.2    Sakai, A.3    Loeb, G.B.4    Ahmad, K.5
  • 60
    • 0014421795 scopus 로고
    • The conformation dependent hydrolysis of DNA by micrococcal nuclease
    • Wingert L, Von Hippel PH: The conformation dependent hydrolysis of DNA by micrococcal nuclease. Biochim. Biophys. Acta 157(1), 114-126 (1968).
    • (1968) Biochim. Biophys. Acta , vol.157 , Issue.1 , pp. 114-126
    • Wingert, L.1    Von Hippel, P.H.2
  • 61
    • 0019888109 scopus 로고
    • High sequence specifcity of micrococcal nuclease
    • Dingwall C, Lomonossoff GP, Laskey RA: High sequence specifcity of micrococcal nuclease. Nucleic Acids Res. 9(12), 2659-2673 (1981).
    • (1981) Nucleic Acids Res , vol.9 , Issue.12 , pp. 2659-2673
    • Dingwall, C.1    Lomonossoff, G.P.2    Laskey, R.A.3
  • 62
    • 38749149152 scopus 로고    scopus 로고
    • Whole-genome sequencing and variant discovery in C
    • Hillier LW, Marth GT, Quinlan AR et al.: Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5(2), 183-188 (2008).
    • (2008) Elegans. Nat. Methods , vol.5 , Issue.2 , pp. 183-188
    • Hillier, L.W.1    Marth, G.T.2    Quinlan, A.R.3
  • 63
    • 34250305146 scopus 로고    scopus 로고
    • Identifcation and ana lysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • Birney E, Stamatoyannopoulos JA, Dutta A et al.: Identifcation and ana lysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146), 799-816 (2007).
    • (2007) Nature , vol.447 , Issue.7146 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3
  • 64
    • 67649292737 scopus 로고    scopus 로고
    • Unlocking the secrets of the genome
    • Celniker SE, Dillon LA, Gerstein MB et al.: Unlocking the secrets of the genome. Nature 459(7249), 927-930 (2009).
    • (2009) Nature , vol.459 , Issue.7249 , pp. 927-930
    • Celniker, S.E.1    Dillon, L.A.2    Gerstein, M.B.3
  • 65
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    • Mikkelsen TS, Ku M, Jaffe DB et al.: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153), 553-560 (2007).
    • (2007) Nature , vol.448 , Issue.7153 , pp. 553-560
    • Mikkelsen, T.S.1    Ku, M.2    Jaffe, D.B.3
  • 66
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
    • Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ: Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319(5), 1097-1113 (2002).
    • (2002) J. Mol. Biol , vol.319 , Issue.5 , pp. 1097-1113
    • Davey, C.A.1    Sargent, D.F.2    Luger, K.3    Maeder, A.W.4    Richmond, T.J.5
  • 67
    • 34447499995 scopus 로고    scopus 로고
    • Structural basis for transcription elongation by bacterial RNA polymerase
    • DOI 10.1038/nature05932, PII NATURE05932
    • Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I: Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448(7150), 157-162 (2007). (Pubitemid 47067370)
    • (2007) Nature , vol.448 , Issue.7150 , pp. 157-162
    • Vassylyev, D.G.1    Vassylyeva, M.N.2    Perederina, A.3    Tahirov, T.H.4    Artsimovitch, I.5
  • 68
    • 0029995880 scopus 로고    scopus 로고
    • Crystal structure of a human TATA box-binding protein/TATA element complex
    • Nikolov DB, Chen H, Halay ED et al.: Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl Acad. Sci. USA 93(10), 4862-4867 (1996).
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , Issue.10 , pp. 4862-4867
    • Nikolov, D.B.1    Chen, H.2    Halay, E.D.3
  • 69
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera-a visualization system for exploratory research and ana lysis
    • Pettersen EF, Goddard TD, Huang CC et al.: UCSF Chimera-a visualization system for exploratory research and ana lysis. J. Comput. Chem. 25(13), 1605-1612 (2004).
    • (2004) J. Comput. Chem , vol.25 , Issue.13 , pp. 1605-1612
    • Pettersen, E.F.1    Goddard, T.D.2    Huang, C.C.3
  • 70
    • 58449116917 scopus 로고    scopus 로고
    • Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
    • Sasaki S, Mello CC, Shimada A et al.: Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323(5912), 401-404 (2009).
    • (2009) Science , vol.323 , Issue.5912 , pp. 401-404
    • Sasaki, S.1    Mello, C.C.2    Shimada, A.3
  • 71
    • 38549131376 scopus 로고    scopus 로고
    • The UCSC Genome Browser Database: 2008 update
    • Database issue
    • Karolchik D, Kuhn RM, Baertsch R et al.: The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36(Database issue), D773-D779 (2008).
    • (2008) Nucleic Acids Res , vol.36
    • Karolchik, D.1    Kuhn, R.M.2    Baertsch, R.3
  • 72
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and ana lysis of the human genome
    • Lander ES, Linton LM, Birren B et al.: Initial sequencing and ana lysis of the human genome. Nature 409(6822), 860-921 (2001).
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2    Birren, B.3


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