메뉴 건너뛰기




Volumn 164, Issue 3, 2014, Pages 1122-1133

A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandemchromatinaffinity purification

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; E2FA PROTEIN, ARABIDOPSIS; HIS HIS HIS HIS HIS HIS; HIS-HIS-HIS-HIS-HIS-HIS; HISTIDINE; OLIGOPEPTIDE; TRANSCRIPTION FACTOR E2F;

EID: 84897624321     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.113.229617     Document Type: Article
Times cited : (26)

References (72)
  • 3
    • 80053388216 scopus 로고    scopus 로고
    • Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq
    • Adli M, Bernstein BE (2011) Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc 6: 1656-1668
    • (2011) Nat Protoc , vol.6 , pp. 1656-1668
    • Adli, M.1    Bernstein, B.E.2
  • 8
    • 11844263147 scopus 로고    scopus 로고
    • The plant-specific cyclin-dependent kinase CDKB1; 1 and transcription factor E2Fa-DPa control the balance of mitotically dividing and endoreduplicating cells in Arabidopsis
    • Boudolf V, Vlieghe K, Beemster GT, Magyar Z, Torres Acosta JA, Maes S, Van Der Schueren E, Inzé D, De Veylder L (2004) The plant-specific cyclin-dependent kinase CDKB1; 1 and transcription factor E2Fa-DPa control the balance of mitotically dividing and endoreduplicating cells in Arabidopsis. Plant Cell 16: 2683-2692
    • (2004) Plant Cell , vol.16 , pp. 2683-2692
    • Boudolf, V.1    Vlieghe, K.2    Beemster, G.T.3    Magyar, Z.4    Torres Acosta, J.A.5    Maes, S.6    Van Der Schueren, E.7    Inzé, D.8    De Veylder, L.9
  • 11
    • 80054697808 scopus 로고    scopus 로고
    • ABAmediated heterophylly is regulated by differential expression of 9-cisepoxycarotenoid dioxygenase 3 in lilies
    • Chen HC, Hwang SG, Chen SM, Shii CT, Cheng WH (2011) ABAmediated heterophylly is regulated by differential expression of 9-cisepoxycarotenoid dioxygenase 3 in lilies. Plant Cell Physiol 52: 1806-1821
    • (2011) Plant Cell Physiol , vol.52 , pp. 1806-1821
    • Chen, H.C.1    Hwang, S.G.2    Chen, S.M.3    Shii, C.T.4    Cheng, W.H.5
  • 12
    • 44949138461 scopus 로고    scopus 로고
    • A rapid micro chromatin immunoprecipitation assay (microChIP)
    • Dahl JA, Collas P (2008) A rapid micro chromatin immunoprecipitation assay (microChIP). Nat Protoc 3: 1032-1045
    • (2008) Nat Protoc , vol.3 , pp. 1032-1045
    • Dahl, J.A.1    Collas, P.2
  • 14
    • 84863780541 scopus 로고    scopus 로고
    • CORNET 2. 0: Integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations
    • De Bodt S, Hollunder J, Nelissen H, Meulemeester N, Inzé D (2012) CORNET 2. 0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. New Phytol 195: 707-720
    • (2012) New Phytol , vol.195 , pp. 707-720
    • De Bodt, S.1    Hollunder, J.2    Nelissen, H.3    Meulemeester, N.4    Inzé, D.5
  • 15
    • 79952199967 scopus 로고    scopus 로고
    • Protein tagging for chromatin immunoprecipitation from Arabidopsis
    • de Folter S (2011) Protein tagging for chromatin immunoprecipitation from Arabidopsis. Methods Mol Biol 678: 199-210
    • (2011) Methods Mol Biol , vol.678 , pp. 199-210
    • de Folter, S.1
  • 16
    • 70350225848 scopus 로고    scopus 로고
    • Dissecting regulatory pathways of G1/S control in Arabidopsis: Common and distinct targets of CYCD3; 1, E2Fa and E2Fc
    • de Jager SM, Scofield S, Huntley RP, Robinson AS, den Boer BG, Murray JA (2009) Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3; 1, E2Fa and E2Fc. Plant Mol Biol 71: 345-365
    • (2009) Plant Mol Biol , vol.71 , pp. 345-365
    • de Jager, S.M.1    Scofield, S.2    Huntley, R.P.3    Robinson, A.S.4    den Boer, B.G.5    Murray, J.A.6
  • 18
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 19
    • 68949213578 scopus 로고    scopus 로고
    • Insights from genomic profiling of transcription factors
    • Farnham PJ (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10: 605-616
    • (2009) Nat Rev Genet , vol.10 , pp. 605-616
    • Farnham, P.J.1
  • 21
  • 22
    • 23744483843 scopus 로고    scopus 로고
    • Profiling histone modification patterns in plants using genomic tiling microarrays
    • Gendrel AV, Lippman Z, Martienssen R, Colot V (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods 2: 213-218
    • (2005) Nat Methods , vol.2 , pp. 213-218
    • Gendrel, A.V.1    Lippman, Z.2    Martienssen, R.3    Colot, V.4
  • 24
    • 33644670152 scopus 로고    scopus 로고
    • An integrated mass spectrometry-based proteomic approach: Quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network
    • Guerrero C, Tagwerker C, Kaiser P, Huang L (2006) An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol Cell Proteomics 5: 366-378
    • (2006) Mol Cell Proteomics , vol.5 , pp. 366-378
    • Guerrero, C.1    Tagwerker, C.2    Kaiser, P.3    Huang, L.4
  • 26
    • 84555189664 scopus 로고    scopus 로고
    • Chromatin affinity purification
    • Harada R, Nepveu A (2012) Chromatin affinity purification. Methods Mol Biol 809: 237-253
    • (2012) Methods Mol Biol , vol.809 , pp. 237-253
    • Harada, R.1    Nepveu, A.2
  • 29
    • 33845634412 scopus 로고    scopus 로고
    • Cell cycle regulation in plant development
    • Inzé D, De Veylder L (2006) Cell cycle regulation in plant development. Annu Rev Genet 40: 77-105
    • (2006) Annu Rev Genet , vol.40 , pp. 77-105
    • Inzé, D.1    De Veylder, L.2
  • 30
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 31
    • 77749320166 scopus 로고    scopus 로고
    • Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)
    • Kaufmann K, Muiño JM, Østerås M, Farinelli L, Krajewski P, Angenent GC (2010) Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protoc 5: 457-472
    • (2010) Nat Protoc , vol.5 , pp. 457-472
    • Kaufmann, K.1    Muiño, J.M.2    Østerås, M.3    Farinelli, L.4    Krajewski, P.5    Angenent, G.C.6
  • 32
    • 64749092881 scopus 로고    scopus 로고
    • Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells
    • Kim J, Cantor AB, Orkin SH, Wang J (2009) Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells. Nat Protoc 4: 506-517
    • (2009) Nat Protoc , vol.4 , pp. 506-517
    • Kim, J.1    Cantor, A.B.2    Orkin, S.H.3    Wang, J.4
  • 33
    • 40749104852 scopus 로고    scopus 로고
    • An extended transcriptional network for pluripotency of embryonic stem cells
    • Kim J, Chu J, Shen X, Wang J, Orkin SH (2008) An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132: 1049-1061
    • (2008) Cell , vol.132 , pp. 1049-1061
    • Kim, J.1    Chu, J.2    Shen, X.3    Wang, J.4    Orkin, S.H.5
  • 34
    • 33646510364 scopus 로고    scopus 로고
    • Genome-wide analysis of protein-DNA interactions
    • Kim TH, Ren B (2006) Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 7: 81-102
    • (2006) Annu Rev Genomics Hum Genet , vol.7 , pp. 81-102
    • Kim, T.H.1    Ren, B.2
  • 36
    • 0033388858 scopus 로고    scopus 로고
    • In vivo cross-linking and immunoprecipitation for studying dynamic protein: DNA associations in a chromatin environment
    • Kuo MH, Allis CD (1999) In vivo cross-linking and immunoprecipitation for studying dynamic protein: DNA associations in a chromatin environment. Methods 19: 425-433
    • (1999) Methods , vol.19 , pp. 425-433
    • Kuo, M.H.1    Allis, C.D.2
  • 38
    • 84878469541 scopus 로고    scopus 로고
    • ANTI-SILENCING FUNCTION1 proteins are involved in ultravioletinduced DNA damage repair and are cell cycle regulated by E2F transcription factors in Arabidopsis
    • Lario LD, Ramirez-Parra E, Gutierrez C, Spampinato CP, Casati P (2013) ANTI-SILENCING FUNCTION1 proteins are involved in ultravioletinduced DNA damage repair and are cell cycle regulated by E2F transcription factors in Arabidopsis. Plant Physiol 162: 1164-1177
    • (2013) Plant Physiol , vol.162 , pp. 1164-1177
    • Lario, L.D.1    Ramirez-Parra, E.2    Gutierrez, C.3    Spampinato, C.P.4    Casati, P.5
  • 39
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 40
    • 29544444954 scopus 로고    scopus 로고
    • The role of the Arabidopsis E2FB transcription factor in regulating auxindependent cell division
    • Magyar Z, De Veylder L, Atanassova A, Bakó L, Inzé D, Bögre L (2005) The role of the Arabidopsis E2FB transcription factor in regulating auxindependent cell division. Plant Cell 17: 2527-2541
    • (2005) Plant Cell , vol.17 , pp. 2527-2541
    • Magyar, Z.1    De Veylder, L.2    Atanassova, A.3    Bakó, L.4    Inzé, D.5    Bögre, L.6
  • 42
    • 1342266280 scopus 로고    scopus 로고
    • Genome-wide gene expression in an Arabidopsis cell suspension
    • Menges M, Hennig L, Gruissem W, Murray JA (2003) Genome-wide gene expression in an Arabidopsis cell suspension. Plant Mol Biol 53: 423-442
    • (2003) Plant Mol Biol , vol.53 , pp. 423-442
    • Menges, M.1    Hennig, L.2    Gruissem, W.3    Murray, J.A.4
  • 43
    • 0037343103 scopus 로고    scopus 로고
    • Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: Identification of genes expressed differentially in epidermal cells or vascular tissues of maize
    • Nakazono M, Qiu F, Borsuk LA, Schnable PS (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 15: 583-596
    • (2003) Plant Cell , vol.15 , pp. 583-596
    • Nakazono, M.1    Qiu, F.2    Borsuk, L.A.3    Schnable, P.S.4
  • 46
    • 33745549658 scopus 로고    scopus 로고
    • Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations
    • O'Neill LP, VerMilyea MD, Turner BM (2006) Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat Genet 38: 835-841
    • (2006) Nat Genet , vol.38 , pp. 835-841
    • O'Neill, L.P.1    VerMilyea, M.D.2    Turner, B.M.3
  • 47
    • 33846231036 scopus 로고    scopus 로고
    • The human synMuv-like protein LIN-9 is required for transcription of G2/M genes and for entry into mitosis
    • Osterloh L, von Eyss B, Schmit F, Rein L, Hübner D, Samans B, Hauser S, Gaubatz S (2007) The human synMuv-like protein LIN-9 is required for transcription of G2/M genes and for entry into mitosis. EMBO J 26: 144-157
    • (2007) EMBO J , vol.26 , pp. 144-157
    • Osterloh, L.1    von Eyss, B.2    Schmit, F.3    Rein, L.4    Hübner, D.5    Samans, B.6    Hauser, S.7    Gaubatz, S.8
  • 48
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680
    • (2009) Nat Rev Genet , vol.10 , pp. 669-680
    • Park, P.J.1
  • 51
    • 77953414532 scopus 로고    scopus 로고
    • Lin9, a subunit of the mammalian DREAM complex, is essential for embryonic development, for survival of adult mice, and for tumor suppression
    • Reichert N, Wurster S, Ulrich T, Schmitt K, Hauser S, Probst L, Götz R, Ceteci F, Moll R, Rapp U, et al (2010) Lin9, a subunit of the mammalian DREAM complex, is essential for embryonic development, for survival of adult mice, and for tumor suppression. Mol Cell Biol 30: 2896-2908
    • (2010) Mol Cell Biol , vol.30 , pp. 2896-2908
    • Reichert, N.1    Wurster, S.2    Ulrich, T.3    Schmitt, K.4    Hauser, S.5    Probst, L.6    Götz, R.7    Ceteci, F.8    Moll, R.9    Rapp, U.10
  • 52
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Séraphin B (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17: 1030-1032
    • (1999) Nat Biotechnol , vol.17 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Séraphin, B.6
  • 54
    • 44949085661 scopus 로고    scopus 로고
    • An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants
    • Saleh A, Alvarez-Venegas R, Avramova Z (2008) An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat Protoc 3: 1018-1025
    • (2008) Nat Protoc , vol.3 , pp. 1018-1025
    • Saleh, A.1    Alvarez-Venegas, R.2    Avramova, Z.3
  • 56
    • 33745456752 scopus 로고    scopus 로고
    • Interplay between Arabidopsis activating factors E2Fb and E2Fa in cell cycle progression and development
    • Sozzani R, Maggio C, Varotto S, Canova S, Bergounioux C, Albani D, Cella R (2006) Interplay between Arabidopsis activating factors E2Fb and E2Fa in cell cycle progression and development. Plant Physiol 140: 1355-1366
    • (2006) Plant Physiol , vol.140 , pp. 1355-1366
    • Sozzani, R.1    Maggio, C.2    Varotto, S.3    Canova, S.4    Bergounioux, C.5    Albani, D.6    Cella, R.7
  • 57
    • 33645703441 scopus 로고    scopus 로고
    • A tandem affinity tag for two-step purification under fully denaturing conditions: Application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking
    • Tagwerker C, Flick K, Cui M, Guerrero C, Dou Y, Auer B, Baldi P, Huang L, Kaiser P (2006) A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking. Mol Cell Proteomics 5: 737-748
    • (2006) Mol Cell Proteomics , vol.5 , pp. 737-748
    • Tagwerker, C.1    Flick, K.2    Cui, M.3    Guerrero, C.4    Dou, Y.5    Auer, B.6    Baldi, P.7    Huang, L.8    Kaiser, P.9
  • 59
    • 38049146018 scopus 로고    scopus 로고
    • Protein characterization of Saccharomyces cerevisiae RNA polymerase II after in vivo cross-linking
    • Tardiff DF, Abruzzi KC, Rosbash M (2007) Protein characterization of Saccharomyces cerevisiae RNA polymerase II after in vivo cross-linking. Proc Natl Acad Sci USA 104: 19948-19953
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 19948-19953
    • Tardiff, D.F.1    Abruzzi, K.C.2    Rosbash, M.3
  • 61
    • 85115107592 scopus 로고
    • Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection
    • Valvekens D, Montagu MV, Van Lijsebettens M (1988) Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc Natl Acad Sci USA 85: 5536-5540
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 5536-5540
    • Valvekens, D.1    Montagu, M.V.2    Van Lijsebettens, M.3
  • 62
    • 50149108858 scopus 로고    scopus 로고
    • Conserved functions of the pRB and E2F families
    • van den Heuvel S, Dyson NJ (2008) Conserved functions of the pRB and E2F families. Nat Rev Mol Cell Biol 9: 713-724
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 713-724
    • van den Heuvel, S.1    Dyson, N.J.2
  • 63
    • 66649122827 scopus 로고    scopus 로고
    • Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
    • Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y (2009) Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol 150: 535-546
    • (2009) Plant Physiol , vol.150 , pp. 535-546
    • Vandepoele, K.1    Quimbaya, M.2    Casneuf, T.3    De Veylder, L.4    Van de Peer, Y.5
  • 68
    • 53149142072 scopus 로고    scopus 로고
    • Boosting tandem affinity purification of plant protein complexes
    • Van Leene J, Witters E, Inzé D, De Jaeger G (2008) Boosting tandem affinity purification of plant protein complexes. Trends Plant Sci 13: 517-520
    • (2008) Trends Plant Sci , vol.13 , pp. 517-520
    • Van Leene, J.1    Witters, E.2    Inzé, D.3    De Jaeger, G.4
  • 71
    • 21444433993 scopus 로고    scopus 로고
    • Uptake, localization, and noncarboxylase roles of biotin
    • Zempleni J (2005) Uptake, localization, and noncarboxylase roles of biotin. Annu Rev Nutr 25: 175-196
    • (2005) Annu Rev Nutr , vol.25 , pp. 175-196
    • Zempleni, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.