메뉴 건너뛰기




Volumn 24, Issue 11, 2014, Pages 1842-1853

Application of histone modification-specific interaction domains as an alternative to antibodies

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE 3A; ANTIBODY; BMI1 PROTEIN; CBX7 PROTEIN, HUMAN; DNA (CYTOSINE 5) METHYLTRANSFERASE; HISTONE; LYSINE; PEPTIDE; PROTEIN BINDING;

EID: 84927129921     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.170985.113     Document Type: Article
Times cited : (53)

References (56)
  • 1
    • 79952534189 scopus 로고    scopus 로고
    • Regulation of chromatin by histone modifications
    • Bannister AJ, Kouzarides T. 2011. Regulation of chromatin by histone modifications. Cell Res 21: 381-395.
    • (2011) Cell Res , vol.21 , pp. 381-395
    • Bannister, A.J.1    Kouzarides, T.2
  • 3
    • 33645231102 scopus 로고    scopus 로고
    • Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin
    • Bernstein E, Duncan EM, Masui O, Gil J, Heard E, Allis CD. 2006. Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol 26: 2560-2569.
    • (2006) Mol Cell Biol , vol.26 , pp. 2560-2569
    • Bernstein, E.1    Duncan, E.M.2    Masui, O.3    Gil, J.4    Heard, E.5    Allis, C.D.6
  • 4
    • 84863256915 scopus 로고    scopus 로고
    • Bio-CAP: A versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA
    • Blackledge NP, Long HK, Zhou JC, Kriaucionis S, Patient R, Klose RJ. 2012. Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. Nucleic Acids Res 40: e32.
    • (2012) Nucleic Acids Res , vol.40 , pp. e32
    • Blackledge, N.P.1    Long, H.K.2    Zhou, J.C.3    Kriaucionis, S.4    Patient, R.5    Klose, R.J.6
  • 6
    • 79151476637 scopus 로고    scopus 로고
    • Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays
    • Bock I, Dhayalan A, Kudithipudi S, Brandt O, Rathert P, Jeltsch A. 2011a. Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays. Epigenetics 6: 256-263.
    • (2011) Epigenetics , vol.6 , pp. 256-263
    • Bock, I.1    Dhayalan, A.2    Kudithipudi, S.3    Brandt, O.4    Rathert, P.5    Jeltsch, A.6
  • 7
    • 80052140473 scopus 로고    scopus 로고
    • Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails
    • Bock I, Kudithipudi S, Tamas R, Kungulovski G, Dhayalan A, Jeltsch A. 2011b. Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails. BMC Biochem 12: 48.
    • (2011) BMC Biochem , vol.12 , pp. 48
    • Bock, I.1    Kudithipudi, S.2    Tamas, R.3    Kungulovski, G.4    Dhayalan, A.5    Jeltsch, A.6
  • 9
    • 40649089223 scopus 로고    scopus 로고
    • Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography
    • Brand M, Rampalli S, Chaturvedi CP, Dilworth FJ. 2008. Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography. Nat Protoc 3: 398-409.
    • (2008) Nat Protoc , vol.3 , pp. 398-409
    • Brand, M.1    Rampalli, S.2    Chaturvedi, C.P.3    Dilworth, F.J.4
  • 10
    • 79955468817 scopus 로고    scopus 로고
    • Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: Potential effect of phosphorylation on methyl-lysine binding
    • Chang Y, Horton JR, Bedford MT, Zhang X, Cheng X. 2011. Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding. J Mol Biol 408: 807-814.
    • (2011) J Mol Biol , vol.408 , pp. 807-814
    • Chang, Y.1    Horton, J.R.2    Bedford, M.T.3    Zhang, X.4    Cheng, X.5
  • 11
    • 0028340280 scopus 로고
    • Purification of CpG islands using a methylated DNA binding column
    • Cross SH, Charlton JA, Nan X, Bird AP. 1994. Purification of CpG islands using a methylated DNA binding column. Nat Genet 6: 236-244.
    • (1994) Nat Genet , vol.6 , pp. 236-244
    • Cross, S.H.1    Charlton, J.A.2    Nan, X.3    Bird, A.P.4
  • 15
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the encyclopedia of DNA elements (ENCODE)
    • The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
    • (2011) PLoS Biol , vol.9 , pp. e1001046
  • 18
    • 70350494322 scopus 로고    scopus 로고
    • Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells
    • Fiskus W, Wang Y, Sreekumar A, Buckley KM, Shi H, Jillella A, Ustun C, Rao R, Fernandez P, Chen J, et al. 2009. Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells. Blood 114: 2733-2743.
    • (2009) Blood , vol.114 , pp. 2733-2743
    • Fiskus, W.1    Wang, Y.2    Sreekumar, A.3    Buckley, K.M.4    Shi, H.5    Jillella, A.6    Ustun, C.7    Rao, R.8    Fernandez, P.9    Chen, J.10
  • 19
    • 79151470871 scopus 로고    scopus 로고
    • Influence of combinatorial histone modifications on antibody and effector protein recognition
    • Fuchs SM, Krajewski K, Baker RW, Miller VL, Strahl BD. 2011. Influence of combinatorial histone modifications on antibody and effector protein recognition. Curr Biol 21: 53-58.
    • (2011) Curr Biol , vol.21 , pp. 53-58
    • Fuchs, S.M.1    Krajewski, K.2    Baker, R.W.3    Miller, V.L.4    Strahl, B.D.5
  • 21
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks J, Nekrutenko A, Taylor J. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
    • (2010) Genome Biol , vol.11 , pp. R86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 22
    • 84866849125 scopus 로고    scopus 로고
    • EpiExplorer: Live exploration and global analysis of large epigenomic datasets
    • Halachev K, Bast H, Albrecht F, Lengauer T, Bock C. 2012. EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol 13: R96.
    • (2012) Genome Biol , vol.13 , pp. R96
    • Halachev, K.1    Bast, H.2    Albrecht, F.3    Lengauer, T.4    Bock, C.5
  • 26
    • 0036134395 scopus 로고    scopus 로고
    • Site-directed mutagenesis by polymerase chain reaction
    • Jeltsch A, Lanio T. 2002. Site-directed mutagenesis by polymerase chain reaction. Methods Mol Biol 182: 85-94.
    • (2002) Methods Mol Biol , vol.182 , pp. 85-94
    • Jeltsch, A.1    Lanio, T.2
  • 30
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides T. 2007. Chromatin modifications and their function. Cell 128: 693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 32
    • 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 SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 33
    • 80053935982 scopus 로고    scopus 로고
    • Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9
    • Li J, Li Z, Ruan J, Xu C, Tong Y, Pan PW, Tempel W, Crombet L, Min J, Zang J. 2011. Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9. PLoS ONE 6: e25104.
    • (2011) PLoS ONE , vol.6 , pp. e25104
    • Li, J.1    Li, Z.2    Ruan, J.3    Xu, C.4    Tong, Y.5    Pan, P.W.6    Tempel, W.7    Crombet, L.8    Min, J.9    Zang, J.10
  • 35
    • 84878825857 scopus 로고    scopus 로고
    • A method for systematic mapping of protein lysine methylation identifies functions for HP1b in DNA damage response
    • Liu H, Galka M, Mori E, Liu X, Lin YF, Wei R, Pittock P, Voss C, Dhami G, Li X, et al. 2013. A method for systematic mapping of protein lysine methylation identifies functions for HP1b in DNA damage response. Mol Cell 50: 723-735.
    • (2013) Mol Cell , vol.50 , pp. 723-735
    • Liu, H.1    Galka, M.2    Mori, E.3    Liu, X.4    Lin, Y.F.5    Wei, R.6    Pittock, P.7    Voss, C.8    Dhami, G.9    Li, X.10
  • 36
    • 77949678340 scopus 로고    scopus 로고
    • Chromatin structure and the inheritance of epigenetic information
    • Margueron R, Reinberg D. 2010. Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11: 285-296.
    • (2010) Nat Rev Genet , vol.11 , pp. 285-296
    • Margueron, R.1    Reinberg, D.2
  • 38
    • 84869237494 scopus 로고    scopus 로고
    • Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay
    • Nishikori S, Hattori T, Fuchs SM, Yasui N, Wojcik J, Koide A, Strahl BD, Koide S. 2012. Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. J Mol Biol 424: 391-399.
    • (2012) J Mol Biol , vol.424 , pp. 391-399
    • Nishikori, S.1    Hattori, T.2    Fuchs, S.M.3    Yasui, N.4    Wojcik, J.5    Koide, A.6    Strahl, B.D.7    Koide, S.8
  • 39
    • 84878944044 scopus 로고    scopus 로고
    • Readout of epigenetic modifications
    • Patel DJ, Wang Z. 2013. Readout of epigenetic modifications. Annu Rev Biochem 82: 81-118.
    • (2013) Annu Rev Biochem , vol.82 , pp. 81-118
    • Patel, D.J.1    Wang, Z.2
  • 40
    • 84861174704 scopus 로고    scopus 로고
    • Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules
    • Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD. 2012. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Mol Cell Proteomics 11: 128-137.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 128-137
    • Peach, S.E.1    Rudomin, E.L.2    Udeshi, N.D.3    Carr, S.A.4    Jaffe, J.D.5
  • 43
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 48
    • 70349871718 scopus 로고    scopus 로고
    • CEAS: Cis-regulatory element annotation system
    • Shin H, Liu T, Manrai AK, Liu XS. 2009. CEAS: cis-regulatory element annotation system. Bioinformatics 25: 2605-2606.
    • (2009) Bioinformatics , vol.25 , pp. 2605-2606
    • Shin, H.1    Liu, T.2    Manrai, A.K.3    Liu, X.S.4
  • 50
    • 84875537133 scopus 로고    scopus 로고
    • Epigenetic reprogramming in cancer
    • Suva ML, Riggi N, Bernstein BE. 2013. Epigenetic reprogramming in cancer. Science 339: 1567-1570.
    • (2013) Science , vol.339 , pp. 1567-1570
    • Suva, M.L.1    Riggi, N.2    Bernstein, B.E.3
  • 52
    • 35848961668 scopus 로고    scopus 로고
    • How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers
    • Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. 2007. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14: 1025-1040.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 1025-1040
    • Taverna, S.D.1    Li, H.2    Ruthenburg, A.J.3    Allis, C.D.4    Patel, D.J.5
  • 55
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    • Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. 2009. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
    • (2009) Bioinformatics , vol.25 , pp. 1952-1958
    • Zang, C.1    Schones, D.E.2    Zeng, C.3    Cui, K.4    Zhao, K.5    Peng, W.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.