综述

植物基因组DNase I超敏感位点的研究进展

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  • 电子科技大学生命科学与技术学院, 成都610054

收稿日期: 2012-12-20

  修回日期: 2013-02-04

  网络出版日期: 2013-07-25

基金资助

国家自然科学基金项目(编号:31171542和31101143)和电子科技大学中央高校业务费项目资助

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

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  • 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

摘要

真核生物的基因表达与调控是一系列顺式作用元件(cis-acting element)与反式作用因子(trans-acting factor)相互作用的结果。顺式作用元件本身不编码蛋白, 只是基因组中一些特定的区域, 它们需与反式作用因子结合才能发挥其生理作用。目前已知, 顺式作用元件往往与染色质的结构密切相关, 能与反式作用因子结合发挥生物学功能的顺式作用元件, 通常存在于脱氧核糖核酸酶I超敏感位点 (DNase I hypersensitive site) 的内部或周围。随着越来越多的植物基因组测序的进展, 大规模高通量鉴定植物基因组的顺式作用元件正在受到关注, 通过鉴定脱氧核糖核酸酶I超敏感位点可以有效确定顺式作用元件的富集区域, 将对功能基因组学研究提供的数据支持。文章综述了近期高通量鉴定和分析植物基因组脱氧核糖核酸酶 I 超敏感位点研究进展。

本文引用格式

张韬 杨足君 . 植物基因组DNase I超敏感位点的研究进展[J]. 遗传, 2013 , 35(7) : 867 -874 . DOI: 10.3724/SP.J.1005.2013.00867

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.

参考文献

[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
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