Felsenfeld G,Groudine M.Controlling the double helix.Nature,2003,421(6921):448-453.
[2]
Kornberg R D.Chromatin structure:a repeating unit of histones and DNA.Science,1974,184(4139):868-871.
[3]
Green C M and Almouzni G.When repair meets chromatin.EMBO Report,2002,3(1):28-33.
[4]
Groth A,Rocha W,Verreault A.Chromatin challenges during DNA replication and repair.Cell,2007,128(4):721-733.
[5]
Gong F,Fahy D,Smerdon M J.Rad4-Rad23 interaction with SWI/SNF links ATP-dependent chromatin remodeling with nucleotide excision repair.Nature Structural & Molecular Biology,2006,13(10):902-907.
[6]
Liu Q,Kasuga M,Sakuma Y,Abe H,Miura S,Yamaguchi-Schinozaki K,Shinozaki K.Two transcription factors,DREB1 and DREB2,with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought-and low-temperature-responsive gene expression,respectively,in Arabidopsis.The Plant Cell,1998,10(8):1931-1406.
[7]
Sims lll,Mandal S S,Reinberg D.Recent highlights of RNA-polymerase-II-mediated transcription.Current Opinion in Cell Biology,2004,16(3):263-271.
[8]
Tihon C.Cyclic AMP-protein-DNA complex formation in mammalian cell-free systems.Journal of Cyclic Nucleotide Research,1977,3(3):207-218.
[9]
Ritzi M,Tillack K,Gerhardt J,Ott E,Humme S,Kremmer E,Hammerschmidt W,Schepers A.Complex protein-DNA dynamics at the latent origin of DNA replication of Epstein-Barr virus.Journal of Cell Science,2003,116(19):3971-3984.
[10]
Zentgraf U,Hinderhofer K,Kolb D.Specific association of a small protein with the telomeric DNA-protein complex during the onset of leaf senescence in Arabidopsis thaliana.Plant Molecular Biology,2000,42(3):429-438.
[11]
Zhou J M,Trifa Y,Silva H.NPR1 differentially interacts with members of the TGA/OBF family of transcription factors that bind an element of the PR-1 gene required for induction by salicylic acid.Molecular Plant-Microbe Interactions,2000,13(2):191-202.
[12]
Ahmad K,Henikoff S.Histone H3 variants specify modes of chromatin assembly.Proceedings of the National Academy of Sciences,2002,10(99):16477-16484.
[13]
Redon C,Pilch D,Rogakou E.Histone H2A variants H2AX and H2AZ.Current Opinion in Genetics & Development,2002,12(2):162-169
[14]
Henikoff S,Furuyama T,Ahmad K.Histone variants,nucleosome assembly and epigenetic inheritance.Trends in Genetics,2004,20(7):320-326.
[15]
Johnson L M,Law J A,Khattar A,Henderson L R,Jacobsen S E.SRA-Domain proteins required for DRM2-Mediated de novo DNA methylation.PLoS Genetics,2008,4(11):e1000280.
[16]
Senear D F,Brenowitz M.Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay.Journal of Biological Chemistry,1991,266(21):13661-13671.
[17]
LeBlanc B,Moss T.DNase Ⅰ Footprinting.Methods in Molecular Biology,2001,30:1-10.
[18]
Galas D J,Schmitz A.DNAse footprinting:a simple method for the detection of protein-DNA binding specificity.Nucleic Acids Research,1978,5(9):3157-3170.
[19]
Shaw P E,Stewart A F.Identification of protein/DNA contacts with dimethyl sulfate:methylation protection and methylation interference.Methods in Molecular Biology,2009,543:97-104.
[20]
Bowler C,Benvenuto G,Laflmme P,Molino D,Probst A V,Tariq M,Paskzkowski J.Chromatin techniques for plant cells.The Plant Journal,2004,39(5):774-789.
[21]
Kuo M H,Allis C D.In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment.Methods,1999,19(3):425-433.
[22]
Orlando V,Paro R.Chromatin multiprotein complexes involved in the maintenance of transcription patterns.Current Opinion in Genetics and Development,1995,5(2):174-179.
Kaufmann K,Muino J M,Osteras M,Farinelli L,Krajewski P,Angenent G C.Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays(ChIP-CHIP).Nature Protocol,2010,5(3):457-472.
[25]
Tariq M,Saze H,Probst A V,Lichota J,Habu Y,Paszkowski J.Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin.Proceedings of the National Academy of Sciences,2003,100(15):8823-8827.
[26]
Ouyang X,Li J,Li G,Li B,Chen B,Shen H,Huang X,Mo X,Wan X,Lin R,Li S,Wang H,Deng X W.Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development.The Plant Cell,2011,23(7):2514-2535.
[27]
Ye Q,Zhu W,Li L,Ma H,Wang X.Brassinosteroids control male fertility by regulating the expression of key genes involved in Arabidopsis anther and pollen development.Proceedings of the National Academy of Sciences,2010,107(13):6100-6105.
[28]
Chua Y L,Channelière S,Mott E.The bromodomain protein GTE6 controls leaf development in Arabidopsis by histone acetylation at ASYMMETRIC LEAVES1.Gene & Development,2005,19(18):2245-2254.
[29]
Nallamilli B R,Zhang J,Mujahid H,Malone B M,Bridges S M,Peng Z.Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis.PLoS Genetics,2013,9(3):1003322.
[30]
Jothi R,Cuddapah S,Barski,Cui K,Zhao K.Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.Nucleic Acids Research,2008,36(16):5221-5231.
[31]
Visel A,Blow M J,Li Z,Zhang T,Akiyama J A,Plajzer-Frick I,Shoukry M,Wright C,Chen F,Afzal V,Ren B,Rubin E M,Pennacchio L A.ChIP-seq accurately predicts tissue-specific activity of enhancers.Nature,2009,457(7231):854-858.
[32]
Valouev A,Johnson D S,Sundquist A,Medina C,Anton E,Batzoglou S,Myers R M,Sidow A.Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.Nature Methods,2008,5(9):829-834.
[33]
Park M Y,Wu G,Gonzalez-suler A,Vaucheret H,Poething R S.Nuclear processing and export of microRNAs in Arabidopsis.Proceedings of the National Academy of Sciences,2005,102(10):3691-3696.
[34]
Gilmour D S and Lis J T.Detecting protein-DNA interactions in vivo:distribution of RNA polymerase on specific bacterial genes.Proceedings of the National Academy of Sciences,1984,82(14):4275-4279.
[35]
Harrington R E.Optical model studies of salt-induced conformational transitions in the nucleosome.Biochemistry,1982,21(6):1177-1186.
[36]
Wilhelm M L,Wilhelm F X.Conformation of nucleosome core particles and chromatin in high salt concentration.Biochemistry,1980,19(18):4327-4331.
