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Volumn 5, Issue 1, 2012, Pages

Rapid genome-scale mapping of chromatin accessibility in tissue

Author keywords

Benzonase; Chromatin accessibility; Cyanase; DNase I; TACh; Tissue

Indexed keywords

BENZONASE; CYANATE HYDROLASE; DEOXYRIBONUCLEASE I; NUCLEASE; UNCLASSIFIED DRUG;

EID: 84862645458     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-5-10     Document Type: Article
Times cited : (29)

References (32)
  • 1
    • 79952184341 scopus 로고    scopus 로고
    • Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
    • 10.1038/ng.759 21258342
    • Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. S John, PJ Sabo, RE Thurman, MH Sung, SC Biddie, TA Johnson, et al. Nat Genet 2011 43 264 268 10.1038/ng.759 21258342
    • (2011) Nat Genet , vol.43 , pp. 264-268
    • John, S.1    Sabo, P.J.2    Thurman, R.E.3    Sung, M.H.4    Biddie, S.C.5    Johnson, T.A.6
  • 2
    • 79959557189 scopus 로고    scopus 로고
    • Determinants of nucleosome organization in primary human cells
    • 10.1038/nature10002 21602827
    • Determinants of nucleosome organization in primary human cells. A Valouev, SM Johnson, SD Boyd, CL Smith, AZ Fire, A Sidow, Nature 2011 474 516 520 10.1038/nature10002 21602827
    • (2011) Nature , vol.474 , pp. 516-520
    • Valouev, A.1    Johnson, S.M.2    Boyd, S.D.3    Smith, C.L.4    Fire, A.Z.5    Sidow, A.6
  • 3
    • 38649099445 scopus 로고    scopus 로고
    • High-resolution mapping and characterization of open chromatin across the genome
    • DOI 10.1016/j.cell.2007.12.014, PII S0092867407016133
    • High-resolution mapping and characterization of open chromatin across the genome. AP Boyle, S Davis, HP Shulha, P Meltzer, EH Margulies, Z Weng, et al. Cell 2008 132 311 322 10.1016/j.cell.2007.12.014 18243105 (Pubitemid 351172431)
    • (2008) Cell , vol.132 , Issue.2 , pp. 311-322
    • Boyle, A.P.1    Davis, S.2    Shulha, H.P.3    Meltzer, P.4    Margulies, E.H.5    Weng, Z.6    Furey, T.S.7    Crawford, G.E.8
  • 4
    • 79954992662 scopus 로고    scopus 로고
    • Adipogenic development is associated with extensive early remodeling of the chromatin landscape and establishment of transcription factor 'hotspots'
    • 10.1038/emboj.2011.65 21427703
    • Adipogenic development is associated with extensive early remodeling of the chromatin landscape and establishment of transcription factor 'hotspots'. R Siersbaek, R Nielsen, S John, MH Sung, S Baek, A Loft, et al. EMBO J 2011 30 1459 1472 10.1038/emboj.2011.65 21427703
    • (2011) EMBO J , vol.30 , pp. 1459-1472
    • Siersbaek, R.1    Nielsen, R.2    John, S.3    Sung, M.H.4    Baek, S.5    Loft, A.6
  • 5
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • 10.1038/nature09906 21441907
    • Mapping and analysis of chromatin state dynamics in nine human cell types. J Ernst, P Kheradpour, TS Mikkelsen, N Shoresh, LD Ward, CB Epstein, et al. Nature 2011 473 43 49 10.1038/nature09906 21441907
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1    Kheradpour, P.2    Mikkelsen, T.S.3    Shoresh, N.4    Ward, L.D.5    Epstein, C.B.6
  • 6
    • 77956276383 scopus 로고    scopus 로고
    • DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    • DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. L Song, GE Crawford, Cold Spring Harb Protoc 2010 2010
    • (2010) Cold Spring Harb Protoc 2010
    • Song, L.1    Crawford, G.E.2
  • 7
    • 0018458970 scopus 로고
    • The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence
    • 10.1016/0092-8674(79)90095-3 455449
    • The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. C Wu, PM Bingham, KJ Livak, R Holmgren, SC Elgin, Cell 1979 16 797 806 10.1016/0092-8674(79)90095-3 455449
    • (1979) Cell , vol.16 , pp. 797-806
    • Wu, C.1    Bingham, P.M.2    Livak, K.J.3    Holmgren, R.4    Elgin, S.C.5
  • 8
    • 0019303186 scopus 로고
    • The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I
    • DOI 10.1038/286854a0
    • The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. C Wu, Nature 1980 286 5776 854 860 10.1038/286854a0 6774262 (Pubitemid 10010150)
    • (1980) Nature , vol.286 , Issue.5776 , pp. 854-860
    • Wu, C.1
  • 9
    • 79952273012 scopus 로고    scopus 로고
    • Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early drosophila development
    • 10.1371/journal.pgen.1001290 21304941
    • Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development. T Kaplan, XY Li, PJ Sabo, S Thomas, JA Stamatoyannopoulos, MD Biggin, et al. PLoS Genet 2011 7 1001290 10.1371/journal.pgen.1001290 21304941
    • (2011) PLoS Genet , vol.7 , pp. 51001290
    • Kaplan, T.1    Li, X.Y.2    Sabo, P.J.3    Thomas, S.4    Stamatoyannopoulos, J.A.5    Biggin, M.D.6
  • 10
    • 0016361516 scopus 로고
    • Actin is the naturally occurring inhibitor of deoxyribonuclease i
    • 10.1073/pnas.71.12.4742 4140510
    • Actin is the naturally occurring inhibitor of deoxyribonuclease I. E Lazarides, U Lindberg, Proc Natl Acad Sci U S A 1974 71 4742 4746 10.1073/pnas.71.12.4742 4140510
    • (1974) Proc Natl Acad Sci U S A , vol.71 , pp. 4742-4746
    • Lazarides, E.1    Lindberg, U.2
  • 11
    • 0025830143 scopus 로고
    • A simpler and better method to cleave chromatin with DNase 1 for hypersensitive site analyses
    • 10.1093/nar/19.11.3157 1676154
    • A simpler and better method to cleave chromatin with DNase 1 for hypersensitive site analyses. AF Stewart, A Reik, G Schutz, Nucleic Acids Res 1991 19 3157 10.1093/nar/19.11.3157 1676154
    • (1991) Nucleic Acids Res , vol.19 , pp. 3157
    • Stewart, A.F.1    Reik, A.2    Schutz, G.3
  • 12
    • 0032145316 scopus 로고    scopus 로고
    • Serratia marcescens and its extracellular nuclease
    • DOI 10.1016/S0378-1097(98)00234-1, PII S0378109798002341
    • Serratia marcescens and its extracellular nuclease. MJ Benedik, U Strych, FEMS Microbiol Lett 1998 165 1 13 10.1111/j.1574-6968.1998.tb13120.x 9711834 (Pubitemid 28359428)
    • (1998) FEMS Microbiology Letters , vol.165 , Issue.1 , pp. 1-13
    • Benedik, M.J.1    Strych, U.2
  • 13
    • 0029084590 scopus 로고
    • Sequence preferences in cleavage of dsDNA and ssDNA by the extracellular Serratia marcescens endonuclease
    • 10.1021/bi00037a040 7547935
    • Sequence preferences in cleavage of dsDNA and ssDNA by the extracellular Serratia marcescens endonuclease. G Meiss, P Friedhoff, M Hahn, O Gimadutdinow, A Pingoud, Biochemistry 1995 34 11979 11988 10.1021/bi00037a040 7547935
    • (1995) Biochemistry , vol.34 , pp. 11979-11988
    • Meiss, G.1    Friedhoff, P.2    Hahn, M.3    Gimadutdinow, O.4    Pingoud, A.5
  • 14
  • 15
    • 77955149398 scopus 로고    scopus 로고
    • Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
    • 10.1101/gr.104356.109 20551221
    • Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. BG Hoffman, G Robertson, B Zavaglia, M Beach, R Cullum, S Lee, et al. Genome Res 2010 20 1037 1051 10.1101/gr.104356.109 20551221
    • (2010) Genome Res , vol.20 , pp. 1037-1051
    • Hoffman, B.G.1    Robertson, G.2    Zavaglia, B.3    Beach, M.4    Cullum, R.5    Lee, S.6
  • 16
  • 17
    • 77952996319 scopus 로고    scopus 로고
    • Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones
    • 10.1126/science.1186777 20508129
    • Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. RB Deal, JG Henikoff, S Henikoff, Science 2010 328 1161 1164 10.1126/science.1186777 20508129
    • (2010) Science , vol.328 , pp. 1161-1164
    • Deal, R.B.1    Henikoff, J.G.2    Henikoff, S.3
  • 18
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • DOI 10.1038/nmeth.1226, PII NMETH.1226
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq. A Mortazavi, B Williams, K Mccue, L Schaeffer, B Wold, Nat Methods 2008 5 621 628 10.1038/nmeth.1226 18516045 (Pubitemid 351911867)
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 19
    • 0019888109 scopus 로고
    • High sequence specificity of micrococcal nuclease
    • 10.1093/nar/9.12.2659 6269057
    • High sequence specificity of micrococcal nuclease. C Dingwall, GP Lomonossoff, RA Laskey, Nucleic Acids Res 1981 9 2659 2673 10.1093/nar/9.12.2659 6269057
    • (1981) Nucleic Acids Res , vol.9 , pp. 2659-2673
    • Dingwall, C.1    Lomonossoff, G.P.2    Laskey, R.A.3
  • 20
    • 79959911826 scopus 로고    scopus 로고
    • Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding
    • 10.1016/j.molcel.2011.06.016 21726817
    • Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. SC Biddie, S John, PJ Sabo, RE Thurman, TA Johnson, RL Schiltz, et al. Mol Cell 2011 43 145 155 10.1016/j.molcel.2011.06. 016 21726817
    • (2011) Mol Cell , vol.43 , pp. 145-155
    • Biddie, S.C.1    John, S.2    Sabo, P.J.3    Thurman, R.E.4    Johnson, T.A.5    Schiltz, R.L.6
  • 21
    • 40849085514 scopus 로고    scopus 로고
    • FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
    • DOI 10.1016/j.cell.2008.01.018, PII S0092867408001189
    • FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. M Lupien, J Eeckhoute, CA Meyer, Q Wang, Y Zhang, W Li, et al. Cell 2008 132 958 970 10.1016/j.cell.2008.01.018 18358809 (Pubitemid 351391952)
    • (2008) Cell , vol.132 , Issue.6 , pp. 958-970
    • Lupien, M.1    Eeckhoute, J.2    Meyer, C.A.3    Wang, Q.4    Zhang, Y.5    Li, W.6    Carroll, J.S.7    Liu, X.S.8    Brown, M.9
  • 22
    • 79953756678 scopus 로고    scopus 로고
    • Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy
    • 10.1016/j.cmet.2011.03.005 21459322
    • Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy. YK Seo, TI Jeon, HK Chong, J Biesinger, X Xie, TF Osborne, Cell Metab 2011 13 367 375 10.1016/j.cmet.2011.03.005 21459322
    • (2011) Cell Metab , vol.13 , pp. 367-375
    • Seo, Y.K.1    Jeon, T.I.2    Chong, H.K.3    Biesinger, J.4    Xie, X.5    Osborne, T.F.6
  • 23
    • 77649086970 scopus 로고    scopus 로고
    • A map of open chromatin in human pancreatic islets
    • 10.1038/ng.530 20118932
    • A map of open chromatin in human pancreatic islets. K Gaulton, T Nammo, L Pasquali, J Simon, PG Giresi, M Fogarty, et al. Nat Genet 2010 42 255 259 10.1038/ng.530 20118932
    • (2010) Nat Genet , vol.42 , pp. 255-259
    • Gaulton, K.1    Nammo, T.2    Pasquali, L.3    Simon, J.4    Giresi, P.G.5    Fogarty, M.6
  • 24
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    • DOI 10.1101/gr.5533506
    • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. PG Giresi, J Kim, RM McDaniell, VR Iyer, JD Lieb, Genome Res 2007 17 877 885 10.1101/gr.5533506 17179217 (Pubitemid 46919722)
    • (2007) Genome Research , vol.17 , Issue.6 , pp. 877-885
    • Giresi, P.G.1    Kim, J.2    McDaniell, R.M.3    Iyer, V.R.4    Lieb, J.D.5
  • 25
    • 80053539409 scopus 로고    scopus 로고
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • 10.1101/gr.121541.111 21750106
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. L Song, Z Zhang, LL Grasfeder, AP Boyle, PG Giresi, BK Lee, et al. Genome Res 2011 21 1757 67 10.1101/gr.121541.111 21750106
    • (2011) Genome Res , vol.21 , pp. 1757-1767
    • Song, L.1    Zhang, Z.2    Grasfeder, L.L.3    Boyle, A.P.4    Giresi, P.G.5    Lee, B.K.6
  • 26
    • 80053144962 scopus 로고    scopus 로고
    • A decade of exploring the cancer epigenome - Biological and translational implications
    • 10.1038/nrc3130 21941284
    • A decade of exploring the cancer epigenome-biological and translational implications. SB Baylin, PA Jones, Nat Rev Cancer 2011 11 726 734 10.1038/nrc3130 21941284
    • (2011) Nat Rev Cancer , vol.11 , pp. 726-734
    • Baylin, S.B.1    Jones, P.A.2
  • 27
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25 19261174
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. B Langmead, C Trapnell, M Pop, SL Salzberg, Genome Biol 2009 10 25 10.1186/gb-2009-10-3-r25 19261174
    • (2009) Genome Biol , vol.10 , pp. 1825
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 29
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • 10.1016/j.molcel.2010.05.004 20513432
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. S Heinz, C Benner, N Spann, E Bertolino, YC Lin, P Laslo, et al. Mol Cell 2010 38 576 589 10.1016/j.molcel.2010.05.004 20513432
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5    Laslo, P.6
  • 30
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • 10.1186/gb-2010-11-8-r86 20738864
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. J Goecks, A Nekrutenko, J Taylor, Genome Biol 2010 11 86 10.1186/gb-2010-11-8-r86 20738864
    • (2010) Genome Biol , vol.11 , pp. 1886
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 31
    • 79961022522 scopus 로고    scopus 로고
    • DNA methylation status predicts cell-type-specific enhancer activity
    • 10.1038/emboj.2011.210 21701563
    • DNA methylation status predicts cell-type-specific enhancer activity. M Wiench, S John, S Baek, TA Johnson, MH Sung, T Escobar, et al. EMBO J 2011 30 3028 3039 10.1038/emboj.2011.210 21701563
    • (2011) EMBO J , vol.30 , pp. 3028-3039
    • Wiench, M.1    John, S.2    Baek, S.3    Johnson, T.A.4    Sung, M.H.5    Escobar, T.6
  • 32
    • 49249110970 scopus 로고    scopus 로고
    • Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
    • 10.1093/nar/gkn382 18611952
    • Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. ED Wederell, M Bilenky, R Cullum, N Thiessen, M Dagpinar, A Delaney, et al. Nucleic Acids Res 2008 36 4549 4564 10.1093/nar/gkn382 18611952
    • (2008) Nucleic Acids Res , vol.36 , pp. 4549-4564
    • Wederell, E.D.1    Bilenky, M.2    Cullum, R.3    Thiessen, N.4    Dagpinar, M.5    Delaney, A.6


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