| [1] Keene MA, Corces V, Lowenhaupt K, Elgin SC. DNase I hypersensitive sites in Drosophila chromatin occur at the 5′ ends of regions of transcription. Proc Natl Acad Sci USA, 1981, 78(1): 143-146.[2] Wu C. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature, 1980, 286(5776): 854-860.[3] Mcghee JD, Wood WI, Dolan M, Engel JD, Felsenfeld G. A 200-base pair region at the 5' end of the chicken adult β-globin gene is accessible to nuclease digestion. Cell, 1981, 27(1): 45-55.[4] Gross DS, Garrard WT. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem, 1988, 57(1): 159-197.[5] Nedospasov SA, Georgiev GP. Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. Biochem Biophys Res Commun, 1980, 92(2): 532-539.[6] Kodama Y, Nagaya S, Shinmyo A, Kato K. Mapping and characterization of DNase I hypersensitive sites in Arabidopsis chromatin. Plant Cell Physiol, 2007, 48(3): 459-470.[7] Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng ZP, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell, 2008, 132(2): 311-322.[8] Fransz P, de Jong H. From nucleosome to chromosome: a dynamic organization of genetic information. Plant J, 2011, 66(1): 4-17.[9] Segal E, Widom J. What controls nucleosome positions? Trends Genet, 2009, 25(8): 335-343.[10] Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu TT, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi RB, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SCR, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature, 2011, 471(7339): 480-485.[11] Sabo PJ, Humbert R, Hawrylycz M, Wallace JC, Dorschner MO, McArthur M, Stamatoyannopoulos JA. Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc Natl Acad Sci USA, 2004, 101(13): 4537-4542.[12] Hesselberth JR, Chen XY, Zhang ZH, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. Global mapping of protein-DNA interactions in vivo by digital genomic foot-printing. Nat Methods, 2009, 6(4): 283-289.[13] Zhang WL, Wu YF, Schnable JC, Zeng ZX, Freeling M, Crawford GE, Jiang JM. High-resolution mapping of open chromatin in the rice genome. Genome Res, 2012, 22(1): 151-162.[14] Zhang WL, Zhang T, Wu YF, Jiang JM. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell, 2012, 24(7): 2719-2731.[15] Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics, 2008, 24(21): 2537-2538.[16] Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, Tanaka M, Morosawa T, Toyoda T. ARTADE2DB: Improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. Plant Cell Physiol, 2011, 52(2): 254-264.[17] Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kawashima M, Satou M, Kim JM, Kobayashi N, Toyoda T, Shinozaki K, Seki M. Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol, 2008, 49(8): 1135-1149.[18] Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J, Tanaka M, Endo TA, Mochizuki Y, Toyoda T, Kamiya Y, Shinozaki K, Nambara E, Seki M. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using |
