[an error occurred while processing this directive]
en

Progress on identification and analysis of DNase I hypersensitive sites in plant genomes

Expand
  • School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China

Received date: 2012-12-20

  Revised date: 2013-02-04

  Online published: 2013-07-25

Abstract

Eukaryotes’s gene expression and regulation relies on the interaction of their cis-acting elements and trans-acting factors. The cis-elements are specific DNA sequences in the genome and frequently located in the untranslated regions. The trans-acting factors are usually considered to be proteins that bind to the cis-acting sequences to regulate gene expression. It is well known that the cis-elements are always associated with DNase I hypersensitive site, which is a signature of open chromatin. The identification of all the functional cis-element using high-throughput method in plant genome has not been initiated in plant genomes. With the rapid achievement of genomics studies, an increasing number of plant genomes have been sequenced. Genome-wide identification of DNase I hypersensitive sites will be a considerably efficient method to locate cis-element in plants, which will provide a vital potential for further plant functional genomics. The present review is to reveal the recent progresses on identification and analysis of DNase I hypersensitive site in plant genomes.

Cite this article

ZHANG Tao YANG Zu-Jun . Progress on identification and analysis of DNase I hypersensitive sites in plant genomes[J]. Hereditas(Beijing), 2013 , 35(7) : 867 -874 . DOI: 10.3724/SP.J.1005.2013.00867

References

[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
Outlines

/