植物PHD结构域蛋白的结构与功能特性

doi:10.16288/j.yczz.20-412

遗传 ›› 2021, Vol. 43 ›› Issue (4): 323-339.doi: 10.16288/j.yczz.20-412

植物PHD结构域蛋白的结构与功能特性

王天一, 王应祥, 尤辰江()

复旦大学生命科学学院,植物科学研究所,上海 200433

收稿日期:2020-12-01 修回日期:2021-02-09 出版日期:2021-04-20 发布日期:2021-04-20
通讯作者: 尤辰江 E-mail:cjyou@fudan.edu.cn
作者简介:王天一,在读博士研究生,研究方向：植物减数分裂。E-mail: 20110700106@fudan.edu.cn
基金资助:
国家自然科学基金项目资助编号(31925005)

Structural and functional characteristics of plant PHD domain-containing proteins

Tianyi Wang, Yingxiang Wang, Chenjiang You()

Institute of Plant Science, College of Life Science, Fudan University, Shanghai 200433, China

Received:2020-12-01 Revised:2021-02-09 Online:2021-04-20 Published:2021-04-20
Contact: You Chenjiang E-mail:cjyou@fudan.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China No(31925005)

摘要/Abstract

摘要：

植物同源结构域(plant homeodomain, PHD)是锌指结构域家族的一类转录调控因子,其最主要的功能是可以识别各种组蛋白修饰密码,包括组蛋白甲基化和乙酰化等;此外PHD结构域还可以与DNA结合。含有PHD结构域的蛋白,或者本身具有组蛋白修饰酶活性,或者可以与各类组蛋白修饰酶相互作用,还有部分与DNA甲基化相关,具有E3泛素连接酶活性,或者还可以作为染色质重塑因子,以各种不同的作用方式,在植物的生长发育过程中发挥了重要的作用。本文主要综述了结合各种类型组蛋白(包括H3K4me3/0、H3K9me3、H3R2和H3K14ac)以及DNA的PHD结构域的结构特点及其结合特异性、PHD结构域在植物中的进化保守性以及植物中已经发现的含有PHD结构域蛋白的功能及作用机制,为进一步了解该类蛋白在植物生长发育过程中如何发挥作用提供了参考。

关键词: PHD结构域, 组蛋白密码, 组蛋白修饰识别, 转录调控, 表观遗传

Abstract:

Plant homeodomain (PHD) is a class of transcription factor in the Zinc finger domain family. The most important function of which is to recognize various histone modifications, including histone methylation and acetylation, etc. They can also bind to DNA. Proteins with PHD domains, some of which possess histone modification enzyme activity, or can interact with histone modification enzymes, and some are associated with DNA methylation, with E3 ubiquitin ligase activity, or even can be chromatin remodeling factors. As transcriptional regulators, they play an important role in plant growth and development. In this review, we summarize the structural features and substrate binding specificity of PHD domains (including H3K4me3/0, H3K9me3, H3R2, H3K14ac) and DNA, the conservation of plant PHD domain in evolution, the molecular mechanism of known PHD domain-containing proteins in plants, providing a reference for further understanding of the involvement of these proteins during plant growth and development.

Key words: plant homeodomain (PHD), histone code, histone modification reader, transcriptional regulation, epigenetics

王天一, 王应祥, 尤辰江. 植物PHD结构域蛋白的结构与功能特性[J]. 遗传, 2021, 43(4): 323-339.

Tianyi Wang, Yingxiang Wang, Chenjiang You. Structural and functional characteristics of plant PHD domain-containing proteins[J]. Hereditas(Beijing), 2021, 43(4): 323-339.

图/表 5

图1

图2

图3

表1

拟南芥中PHD蛋白的特征与功能"

分类依据		蛋白名称	其他包含的结构域	识别的配体	作用特点	在植物中的功能	参考文献
本身具有组蛋白修饰酶活性	本身具有组蛋白甲基转移酶活性	ATX1	ePHD结构域、SET结构域	H3K4me3	使H3K4三甲基化	根系、叶片和花器官的发育以及一些逆境胁迫基因的转录调控	[29~31]
		ATX2	ePHD结构域、SET结构域	H3K4me2	使H3K4三甲基化	与ATX1拥有相似的序列,但是在调控基因转录方面具有非冗余的功能	[32]
		ATX3/4/5	编码了一个可能的H3K4甲基转移酶	H3K4me2/3	是迄今为止在拟南芥基因组中发现的具有H3K4me2甲基转移酶活性的蛋白	ATX3/4/5具有冗余的功能,可以调控一系列作用于营养生长和生殖生长的基因	[33,34]
		ATXR	SET结构域	H3K4me0	PHD结构域作用于SET结构域结合辅因子以及促进H3K27me1的过程	作用于植物中染色质结构、基因沉默和异染色质的DNA复制过程	[35]
	本身具有组蛋白乙酰基转移酶活性	IDM1/ ROS4	MBD结构域、乙酰基转移酶结构域	H3K4me0	PHD结构域影响IDM1乙酰转移酶的活性	对于DNA去甲基化具有负面调控,阻止高度同源的多拷贝基因和其他重复序列的DNA高度甲基化	[36,37]
与组蛋白修饰酶相互作用	与组蛋白去乙酰化酶相互作用	EBS/SHL	BAH结构域	H3K4me2/3	PHD结构域结合HDA6	作用于开花调控和种子休眠	[38,39]
	与组蛋白甲基转移酶相互作用	MMD1	MMD结构域	H3K4me2/3	与组蛋白去甲基化酶JMJ16相互作用	植物减数分裂,调控浓缩等过程的蛋白	[40~42]
		AL		除AL3以外所有AL蛋白都结合H3K4me2/3	是植物中特有的一类转录因子,PHD结构域与PRC1蛋白相互作用,招募PRC2从而积累H3K27me3	调控植物的生长发育,以及应对低温、干旱、高盐等非生物胁迫	[43~46]
		VIN3		H3K9me2和H3K4me2	PHD结构域与PRC2的相互作用,PHD-PRC2复合体使H3K27me3水平升高	作用于春化作用所需的FLC表观遗传学基因沉默过程	[47~51]
与DNA甲基化相关	结合甲基化的DNA	MBD9	MBD结构域 Bromo结构域	DNA甲基化	MBD结构域结合甲基化的DNA,Bromo结构域可能发挥了催化组蛋白乙酰化反应的作用	通过DNA甲基化和组蛋白乙酰基化,分别间接和直接调控基因的表达,影响拟南芥的生长发育	[52,53]
与DNA甲基化相关	结合甲基化的DNA	ORTH	RING结构域、SRA结构域	DNA甲基化	SRA结构域作用于结合甲基化的DNA	作用于调控DNA甲基化	[54,55]
具有E3泛素连接酶活性		SIZ1	RING、SAP、SXS、PINIT 结构域	H3R2me2和H3K4me3	PHD结构域与染色质重塑复合体有关,也可能作为一个E3泛素连接酶	通过调控基因的表达,作用于植物的生长发育以及应对干旱、低盐的胁迫的过程	[56~58]
是染色质重塑因子		CHR4	Chromodomain结构域		是依赖于ATP的染色质重塑因子	植物的生长发育和DNA损伤应答	[59,60]
是染色质重塑因子		PKL	Chromodomain结构域		是依赖于ATP的染色质重塑因子	DNA损伤应答,以及调控植物生长和响应胁迫基因的表达	[61,62]
与bHLH型的转录因子相互作用		OBE		可能结合 bHLH型的转录因子	促进依赖于转录因子MP的基因的激活表达	在生长素介导的调控发育过程中,作用于根系和顶端分生组织的维持和建立	[63~65]
其他		SCC2	在陆地植物有PHD,动物和真菌中没有	未修饰及甲基化的H3、H4和H2A		作用于减数分裂过程,介导染色质黏连蛋白cohesin的招募过程	[66]
		ORC	只有植物的ORC1中含有PHD结构域	H3K4me3,更倾向于结合未修饰的H3	通过PHD结构域识别靶基因启动子区域的H3K4me3来激活基因的转录表达	作用于DNA复制的起始,在细胞周期中调控转录过程	[67,68]
		MS1				调控作用于花粉外壁形成,花粉细胞溶质和绒毡层的基因的表达,对于减数分裂后的花粉和绒毡层的发育具有重要作用	[69]
		PTM	DDT 结构域	H3K4me3	结合到ABI4的启动子上,以激活ABI4基因的表达。	结合叶绿体被膜的转录调控因子,作用于将叶绿体信号传递到细胞膜	[70]

表1

图4

参考文献 96

[1]	Mouriz A, Lopez-Gonzalez L, Jarillo JA, Piñeiro M. PHDs govern plant development. Plant Signal Behav, 2015,10(7):e993253. doi: 10.4161/15592324.2014.993253 pmid: 26156103
[2]	Zhao S, Zhang BC, Yang M, Zhu JS, Li HT. Systematic profiling of histone readers in Arabidopsis thaliana. Cell Rep, 2018,22(4):1090-1102. doi: 10.1016/j.celrep.2017.12.099 pmid: 29386129
[3]	Pascual J, Martinez-Yamout M, Dyson HJ, Wright PE. Structure of the PHD zinc finger from human Williams- Beuren syndrome transcription factor. J Mol Biol, 2000,304(5):723-729. doi: 10.1006/jmbi.2000.4308 pmid: 11124022
[4]	Kwan AHY, Gell DA, Verger A, Crossley M, Matthews JM, Mackay JP. Engineering a protein scaffold from a PHD finger. Structure, 2003,11(7):803-813. doi: 10.1016/s0969-2126(03)00122-9 pmid: 12842043
[5]	Li HT, Ilin S, Wang W, Duncan E M, Wysocka J, Allis CD, Patel DJ. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature, 2006,442(7098):91-95. doi: 10.1038/nature04802 pmid: 16728978
[6]	Champagne KS, Kutateladze TG. Structural insight into histone recognition by the ING PHD fingers. Curr Drug Targets, 2009,10(5):432-441. doi: 10.2174/138945009788185040 pmid: 19442115
[7]	Xi QR, Wang ZX, Zaromytidou AI, Zhang XH, Chow- Tsang LF, Liu JX, Kim H, Barlas A, Manova-Todorova K, Kaartinen V, Studer L, Mark W, Patel DJ, Massague J. A poised chromatin platform for TGF-β access to master regulators. Cell, 2011,147(7):1511-1524. doi: 10.1016/j.cell.2011.11.032
[8]	Iwase S, Xiang B, Ghosh S, Ren T, Lewis PW, Cochrane JC, Allis CD, Picketts DJ, Patel DJ, Li H, Shi Y. ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nat Struct Mol Biol, 2011,18(7):769-776. doi: 10.1038/nsmb.2062 pmid: 21666679
[9]	Mansfield RE, Musselman CA, Kwan AH, Oliver SS, Garske AL, Davrazou F, Denu JM, Kutateladze TG, Mackay JP. Plant homeodomain (PHD) fingers of CHD4 are histone h3-binding modules with preference for unmodified H3K4 and methylated H3K9. J Biol Chem, 2011,286(13):11779-11791. doi: 10.1074/jbc.M110.208207 pmid: 21278251
[10]	Shi XB, Kachirskaia I, Walter KL, Kuo JA, Lake A, Davrazou F, Chan SM, Martin DGE, Fingerman IM, Briggs SD, Howe L, Utz PJ, Kutateladze TG, Lugovskoy AA, Bedford MT, Gozani O. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J Biol Chem, 2007,282(4):2450-2455. doi: 10.1074/jbc.C600286200 pmid: 17142463
[11]	Hu L, Li Z, Wang P, Lin Y, Xu Y. Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2. Cell Res, 2011,21(9):1374-1378. doi: 10.1038/cr.2011.124 pmid: 21808300
[12]	Wang CK, Shen J, Yang ZZ, Chen P, Zhao B, Hu W, Lan WX, Tong XT, Wu HM, Li GH, Cao CY. Structural basis for site-specific reading of unmodified R2 of histone H3 tail by UHRF1 PHD finger. Cell Res, 2011,21(9):1379-1382. doi: 10.1038/cr.2011.123 pmid: 21808299
[13]	Qiu Y, Liu L, Zhao C, Han CC, Li FD, Zhang JH, Wang Y, Li GH, Mei YD, Wu M, Wu JH, Shi YY. Combinatorial readout of unmodified H3R2 and acetylated H3K14 by the tandem PHD finger of MOZ reveals a regulatory mechanism for HOXA9 transcription. Genes Dev, 2012,26(12):1376-1391. doi: 10.1101/gad.188359.112 pmid: 22713874
[14]	Zeng L, Zhang Q, Li Sd, Plotnikov AN, Walsh MJ, Zhou M. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature, 2010,466(7303):258-262. doi: 10.1038/nature09139 pmid: 20613843
[15]	Wang ZX, Patel DJ. Combinatorial readout of dual histone modifications by paired chromatin-associated modules. J Biol Chem, 2011,286(21):18363-18368. doi: 10.1074/jbc.R111.219139 pmid: 21454653
[16]	Ruthenburg AJ, Li HT, Milne TA, Dewell S, Mcginty RK, Yuen M, Ueberheide B, Dou YL, Muir TW, Patel DJ, Allis CD. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell, 2011,145(5):692-706.
[17]	Sanchez R, Zhou MM. The PHD finger: A versatile epigenome reader. Trends Biochem Sci, 2011,36(7):364-372. doi: 10.1016/j.tibs.2011.03.005 pmid: 21514168
[18]	Gatchalian J, Kutateladze TG. PHD fingers as histone readers. Histone Recognition, Zhou M, Cham:Springer International Publishing, 2015, 27-47.
[19]	Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi XB, Gozani O, Cheng XD, Shi Y. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature, 2007,448(7154):718-722. doi: 10.1038/nature06034 pmid: 17687328
[20]	Chakravarty S, Zeng L, Zhou M. Structure and Site-Specific recognition of histone h3 by the PHD finger of human autoimmune regulator. Structure, 2009,17(5):670-679. doi: 10.1016/j.str.2009.02.017
[21]	Argentaro A, Yang JC, Chapman L, Kowalczyk MS, Gibbons RJ, Higgs DR, Neuhaus D, Rhodes D. Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX. Proc Natl Acad Sci USA, 2007,104(29):11939-11944. doi: 10.1073/pnas.0704057104 pmid: 17609377
[22]	Hung T, Binda O, Champagne KS, Kuo AJ, Johnson K, Chang HY, Simon MD, Kutateladze TG, Gozani O. ING4 mediates crosstalk between histone h3 k4 trimethylation and h3 acetylation to attenuate cellular transformation. Mol Cell, 2009,33(2):248-256. doi: 10.1016/j.molcel.2008.12.016 pmid: 19187765
[23]	Peña PV, Davrazou F, Shi XB, Walter KL, Verkhusha VV, Gozani O, Zhao R, Kutateladze TG. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature, 2006,442(7098):100-103. doi: 10.1038/nature04814 pmid: 16728977
[24]	Iwase S, Xiang B, Ghosh S, Ren T, Lewis PW, Cochrane JC, Allis CD, Picketts DJ, Patel DJ, Li H, Shi Y. ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nat Struct Mol Biol, 2011,18(7):769-776. doi: 10.1038/nsmb.2062 pmid: 21666679
[25]	Li HT, Ilin S, Wang W, Duncan EM, Wysocka J, Allis CD, Patel DJ. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature, 2006,442(7098):91-95. doi: 10.1038/nature04802 pmid: 16728978
[26]	Li W, Zhao A, Tempel W, Loppnau P, Liu Y. Crystal structure of DPF3b in complex with an acetylated histone peptide. J Struct Biol, 2016,195(3):365-372. doi: 10.1016/j.jsb.2016.07.001 pmid: 27402533
[27]	Liu L, Qin S, Zhang JH, Ji P, Shi YY, Wu JH. Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA. J Struct Biol, 2012,180(1):165-173. doi: 10.1016/j.jsb.2012.06.014
[28]	Qin S, Jin L, Zhang JH, Liu L, Ji P, Wu M, Wu JH, Shi YY. Recognition of unmodified histone h3 by the first PHD finger of Bromodomain-PHD finger protein 2 provides insights into the regulation of histone acetyltransferases monocytic leukemic zinc-finger protein (MOZ) and MOZ-related factor (MORF). J Biol Chem, 2011,286(42):36944-36955. doi: 10.1074/jbc.M111.244400 pmid: 21880731
[29]	Napsucialy-Mendivil S, Alvarez-Venegas R, Shishkova S, Dubrovsky JG. ARABIDOPSIS HOMOLOG of TRITHORAX1(ATX1) is required for cell production, patterning, and morphogenesis in root development. J Exp Bot, 2014,65(22):6373-6384. doi: 10.1093/jxb/eru355
[30]	Ding Y, Ndamukong I, Xu ZS, Lapko H, Fromm M, Avramova Z. ATX1-generated H3K4me3 is required for efficient elongation of transcription, not initiation, at ATX1-regulated genes. PLoS Genet, 2012,8(12):e1003111. doi: 10.1371/journal.pgen.1003111 pmid: 23284292
[31]	Ding Y, Avramova Z, Fromm M. Two distinct roles of ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1) at promoters and within transcribed regions of ATX1-Regulated genes. Plant Cell, 2012,23(1):350-363. doi: 10.1105/tpc.110.080150 pmid: 21266657
[32]	Saleh A, Alvarez-Venegas R, Yilmaz M, Le O, Hou GC, Sadder M, Al-Abdallat A, Xia YN, Lu GQ, Ladunga I, Avramova Z. The highly similar arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions. Plant Cell, 2008,20(3):568-579. doi: 10.1105/tpc.107.056614 pmid: 18375658
[33]	Liu Y, Zhang A, Yin H, Meng Q, Yu X, Huang S, Wang J, Ahmad R, Liu B, Xu ZY. Trithorax‐group proteins ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5 function in abscisic acid and dehydration stress responses. New Phytol, 2018,217(4):1582-1597. doi: 10.1111/nph.14933 pmid: 29250818
[34]	Chen LQ, Luo JH, Cui ZH, Xue M, Wang L, Zhang XY, Pawlowski WP, He Y. ATX3, ATX4, and ATX5 encode putative H3K4 methyltransferases and are critical for plant development. Plant Physiol, 2017,174(3):1795-1806. doi: 10.1104/pp.16.01944 pmid: 28550207
[35]	Jacob Y, Feng S, Leblanc CA, Bernatavichute YV, Stroud H, Cokus S, Johnson LM, Pellegrini M, Jacobsen SE, Michaels SD. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol, 2009,16(7):763-768. doi: 10.1038/nsmb.1611 pmid: 19503079
[36]	Li Q, Wang XK, Sun H, Zeng J, Cao ZD, Li Y, Qian WQ. Regulation of active DNA demethylation by a Methyl- CpG-Binding domain protein in arabidopsis thaliana. PLoS Genet, 2015,11(5):e1005210. doi: 10.1371/journal.pgen.1005210 pmid: 25933434
[37]	Qian WQ, Miki D, Lei MG, Zhu XH, Zhang HM, Liu YH, Li Y, Lang ZB, Wang J, Tang K, Liu RY, Zhu JK. Regulation of active DNA demethylation by an alpha- crystallin domain protein in Arabidopsis. Mol Cell, 2014,55(3):361-371. doi: 10.1016/j.molcel.2014.06.008 pmid: 25002145
[38]	Qian S, Lv X, Scheid RN, Lu L, Yang Z, Chen W, Liu R, Boersma MD, Denu JM, Zhong X, Du J. Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nat Commun, 2018,9(1):2425. doi: 10.1038/s41467-018-04836-y pmid: 29930355
[39]	Narro-Diego L, López-González L, Jarillo JA, Piñeiro M. The PHD-containing protein EARLY BOLTING in SHORT DAYS regulates seed dormancy in Arabidopsis. Plant Cell Environ, 2017,40(10):2393-2405. doi: 10.1111/pce.13046 pmid: 28770581
[40]	Yang XH, Makaroff CA, Ma H. The arabidopsis MALE MEIOCYTE DEATH1 gene encodes a PHD-Finger protein that is required for male meiosis. Plant Cell, 2003,15(6):1281-1295. pmid: 12782723
[41]	Wang J, Niu B, Huang J, Wang H, Yang X, Dong A, Makaroff C, Ma H, Wang Y. The PHD finger protein MMD1/DUET ensures the progression of male meiotic chromosome condensation and directly regulates the expression of the condensin gene CAP-D3. Plant Cell, 2016,28(8):1894-1909. doi: 10.1105/tpc.16.00040 pmid: 27385818
[42]	Wang J, Yu CY, Zhang SB, Ye JY, Dai H, Wang HK, Huang JY, Cao XF, Ma JB, Ma H, Wang YX. Cell-type- dependent histone demethylase specificity promotes meiotic chromosome condensation in Arabidopsis. Nat Plants, 2020,6(7):823-837. doi: 10.1038/s41477-020-0697-0 pmid: 32572214
[43]	Molitor AM, Bu ZY, Yu Y, Shen WH. Arabidopsis AL PHD-PRC1 complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes. PLoS Genet, 2014,10(1):e1004091. doi: 10.1371/journal.pgen.1004091 pmid: 24465219
[44]	Nulu NPC, Sundaravelpandian K, Yu SM, Schmidt W. ALFIN-LIKE 6 is involved in root hair elongation during phosphate deficiency in Arabidopsis. New Phytol, 2013,198(3):709-720. doi: 10.1111/nph.12194
[45]	Lee WY, Lee D, Chung W, Kwon CS. Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers. Plant J, 2009,58(3):511-524. doi: 10.1111/j.1365-313X.2009.03795.x pmid: 19154204
[46]	Wei W, Zhang YQ, Tao JJ, Chen HW, Li QT, Zhang WK, Ma B, Lin Q, Zhang JS, Chen SY. The Alfin-like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis. Plant J, 2015,81(6):871-883. doi: 10.1111/tpj.12773 pmid: 25619813
[47]	Kim DH, Sung S. Coordination of the vernalization response through a VIN3 and FLC gene family regulatory network in arabidopsis. Plant Cell, 2013,25(2):454-469. doi: 10.1105/tpc.112.104760
[48]	Kim DH, Sung S. The binding specificity of the PHD-Finger domain of VIN3 moderates vernalization response. Plant Physiol, 2017,173(2):1258-1268. doi: 10.1104/pp.16.01320 pmid: 27999085
[49]	Sung S, Amasino RM. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature, 2004,427(6970):159-164. doi: 10.1038/nature02195 pmid: 14712276
[50]	Bond DM, Wilson IW, Dennis ES, Pogson BJ, Jean Finnegan E. VERNALIZATION INSENSITIVE 3 (VIN3) is required for the response of Arabidopsis thaliana seedlings exposed to low oxygen conditions. Plant J, 2009,59(4):576-587. doi: 10.1111/j.1365-313X.2009.03891.x pmid: 19392705
[51]	Kim DH, Zografos BR, Sung S. Vernalization-Mediated VIN3 induction overcomes the LIKE-HETEROCHROMATIN PROTEIN1/POLYCOMB REPRESSION COMPLEX2- Mediated epigenetic repression. Plant Physiol, 2010,154(2):949-957. doi: 10.1104/pp.110.161083 pmid: 20671111
[52]	Yaish MWF, Peng M, Rothstein SJ. AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation. Plant J, 2009,59(1):123-135. doi: 10.1111/j.1365-313X.2009.03860.x pmid: 19419532
[53]	Peng M, Cui Y, Bi YM, Rothstein SJ. AtMBD9: A protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis. Plant J, 2006,46(2):282-296. doi: 10.1111/j.1365-313X.2006.02691.x pmid: 16623890
[54]	Kim J, Kim JH, Richards EJ, Chung KM, Woo HR. Arabidopsis VIM proteins regulate epigenetic silencing by modulating DNA methylation and histone modification in cooperation with MET1. Mol Plant, 2014,7(9):1470-1485. doi: 10.1093/mp/ssu079
[55]	Kraft E, Bostick M, Jacobsen S E, Callis J. ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Plant J, 2008,56(5):704-715. doi: 10.1111/j.1365-313X.2008.03631.x pmid: 18643997
[56]	Shindo H, Suzuki R, Tsuchiya W, Taichi M, Nishiuchi Y, Yamazaki T. PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2. FEBS Lett, 2012,586(13):1783-1789. doi: 10.1016/j.febslet.2012.04.063
[57]	Catala R, Ouyang J, Abreu IA, Hu YX, Seo H, Zhang XR, Chua NH. The arabidopsis e3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell, 2007,19(9):2952-2966. doi: 10.1105/tpc.106.049981 pmid: 17905899
[58]	Miura K, Rus A, Sharkhuu A, Yokoi S, Karthikeyan AS, Raghothama KG, Baek D, Koo YD, Jin JB, Bressan RA, Yun DJ, Hasegawa PM. The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. Proc Natl Acad Sci USA, 2005,102(21):7760-7765. doi: 10.1073/pnas.0500778102 pmid: 15894620
[59]	Shaked H, Avivi-Ragolsky N, Levy AA. Involvement of the arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination. Genetics, 2006,173(2):985-994. doi: 10.1534/genetics.105.051664 pmid: 16547115
[60]	Hu Y, Lai Y, Zhu D. Transcription regulation by CHD proteins to control plant development. Front Plant Sci, 2014,5:223. doi: 10.3389/fpls.2014.00223 pmid: 24904618
[61]	Murawska M, Brehm A. CHD chromatin remodelers and the transcription cycle. Transcription, 2011,2(6):244-253. doi: 10.4161/trns.2.6.17840 pmid: 22223048
[62]	Zhang H, Bishop B, Ringenberg W, Muir WM, Ogas J. The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone h3 lysine 27. Plant Physiol, 2012,159(1):418-432. doi: 10.1104/pp.112.194878
[63]	Thomas CL, Schmidt D, Bayer EM, Dreos R, Maule AJ. Arabidopsis plant homeodomain finger proteins operate downstream of auxin accumulation in specifying the vasculature and primary root meristem. Plant J, 2009,59(3):426-436. doi: 10.1111/j.1365-313X.2009.03874.x pmid: 19392692
[64]	Saiga S, Möller B, Watanabe-Taneda A, Abe M, Weijers D, Komeda Y. Control of embryonic meristem initiation in Arabidopsis by PHD-finger protein complexes. Development, 2012,139(8):1391-1398. doi: 10.1242/dev.074492 pmid: 22378640
[65]	Saiga S, Furumizu C, Yokoyama R, Kurata T, Sato S, Kato T, Tabata S, Suzuki M, Komeda Y. The Arabidopsis OBERON1 and OBERON2 genes encode plant homeodomain finger proteins and are required for apical meristem maintenance. Development, 2008,135(10):1751-1759. doi: 10.1242/dev.014993 pmid: 18403411
[66]	Wang HK, Xu WY, Sun YJ, Lian QC, Wang C, Yu CY, He CP, Wang J, Ma H, Copenhaver G P, Wang Y. The cohesin loader SCC2 contains a PHD finger that is required for meiosis in land plants. Plos Genet, 2020,16(6):e1008849. doi: 10.1371/journal.pgen.1008849 pmid: 32516352
[67]	de la Paz Sanchez M, Gutierrez C, Dean C. Arabidopsis ORC1 is a PHD-Containing H3K4me3 effector that regulates transcription. Proc Natl Acad Sci USA, 2009,106(6):2065-2070. doi: 10.1073/pnas.0811093106 pmid: 19171893
[68]	Li SS, Yang ZL, Du X, Liu R, Wilkinson AW, Gozani O, Jacobsen SE, Patel DJ, Du J. Structural basis for the unique multivalent readout of unmodified h3 tail by arabidopsis ORC1b BAH-PHD cassette. Structure, 2016,24(3):486-494. doi: 10.1016/j.str.2016.01.004 pmid: 26876097
[69]	Ito T, Nagata N, Yoshiba Y, Ohme-Takagi M, Ma H, Shinozaki K. Arabidopsis MALE STERILITY1 encodes a PHD-Type transcription factor and regulates pollen and tapetum development. Plant Cell, 2007,19(11):3549-3562. doi: 10.1105/tpc.107.054536 pmid: 18032630
[70]	Sun X, Feng P, Xu X, Guo H, Ma J, Chi W, Lin R, Lu C, Zhang L. A chloroplast envelope-bound PHD transcription factor mediates chloroplast signals to the nucleus. Nat Commun, 2011,2:477. doi: 10.1038/ncomms1486 pmid: 21934661
[71]	Alvarez-Venegas R, Sadder M, Hlavacka A, Baluska F, Xia YN, Lu GQ, Firsov A, Sarath G, Moriyama H, Dubrovsky JG, Avramova Z. The arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-Phosphate, and the two regulate a common set of target genes. Proc Natl Acad Sci USA, 2006,103(15):6049-6054. doi: 10.1073/pnas.0600944103 pmid: 16585509
[72]	Jacob Y, Stroud H, Leblanc C, Feng SH, Zhuo LT, Caro E, Hassel C, Gutierrez C, Michaels SD, Jacobsen SE. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature, 2010,466(7309):987-991. doi: 10.1038/nature09290 pmid: 20631708
[73]	He C, Liu N, Xie DY, Liu YH, Xiao YZ, Li FD. Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1. Biochem J, 2019,476(13):1957-1973. doi: 10.1042/BCJ20190091 pmid: 31253666
[74]	Fortschegger K, Shiekhattar R. Plant homeodomain fingers form a helping hand for transcription. Epigenetics, 2011,6(1):4-8. doi: 10.4161/epi.6.1.13297
[75]	Qian WQ, Miki D, Zhang H, Liu YH, Zhang X, Tang K, Kan YC, La HG, Li XJ, Li SF, Zhu XH, Shi XB, Zhang KL, Pontes O, Chen XM, Liu RY, Gong ZZ, Zhu JK. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science, 2012,336(6087):1445-1448. doi: 10.1126/science.1219416 pmid: 22700931
[76]	Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li HT, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD. Yng1 PHD finger binding to h3 trimethylated at k4 promotes NuA3 HAT activity at k14 of h3 and transcription at a subset of targeted ORFs. Mol Cell, 2006,24(5):785-796. doi: 10.1016/j.molcel.2006.10.026 pmid: 17157260
[77]	Müssig C, Kauschmann A, Clouse SD, Altmann T. The Arabidopsis PHD-finger protein SHL is required for proper development and fertility. Mol Gen Genet, 2000,264(4):363-370. doi: 10.1007/s004380000313 pmid: 11129039
[78]	Fornara F, de Montaigu A, Coupland G. SnapShot: Control of flowering in arabidopsis. Cell, 2010,141(3):550. doi: 10.1016/j.cell.2010.04.024 pmid: 20434991
[79]	López-González L, Mouriz A, Narro-Diego L, Bustos R, Martínez-Zapater JM, Jarillo JA, Piñeiro M. Chromatin- Dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-Containing proteins. Plant Cell, 2014,26(10):3922-3938. doi: 10.1105/tpc.114.130781
[80]	Liu P, Zhang SB, Zhou B, Luo X, Zhou XF, Cai B, Jin YH, Niu D, Lin JX, Cao XF, Jin JB. The histone H3K4 demethylase JMJ16 represses leaf senescence in Arabidopsis. Plant Cell, 2019,31(2):430-443. doi: 10.1105/tpc.18.00693 pmid: 30712008
[81]	Laugesen A, Højfeldt JW, Helin K. Molecular mechanisms directing PRC2 recruitment and H3K27 methylation. Mol Cell, 2019,74(1):8-18. doi: 10.1016/j.molcel.2019.03.011 pmid: 30951652
[82]	Lucia FD, Crevillen P, Alexandra MEJ, Greb T, Dean C. A PHD-Polycomb Repressive Complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci USA, 2008,105(44):16831-16836. doi: 10.1073/pnas.0808687105 pmid: 18854416
[83]	Sarma K, Margueron R, Ivanov A, Pirrotta V, Reinberg D. Ezh2 requires PHF1 to efficiently catalyze h3 lysine 27 trimethylation in vivo. Mol Cell Biol, 2008,28(8):2718-2731. doi: 10.1128/MCB.02017-07 pmid: 18285464
[84]	Nekrasov M, Klymenko T, Fraterman S, Papp B, Oktaba K, Kocher T, Cohen A, Stunnenberg HG, Wilm M, Muller J. Pcl-PRC2 is needed to generate high levels of H3-K27 trimethylation at Polycomb target genes. Embo J, 2007,26(18):4078-4088. doi: 10.1038/sj.emboj.7601837 pmid: 17762866
[85]	O'Connell S, Wang L, Robert S, Jones CA, Saint R, Jones RS. Polycomblike PHD fingers mediate conserved interaction with enhancer of zeste protein. J Biol Chem, 2001,276(46):43065-43073. doi: 10.1074/jbc.M104294200 pmid: 11571280
[86]	Musselman CA, Avvakumov N, Watanabe R, Abraham CG, Lalonde ME, Hong Z, Allen C, Roy S, Nuñez JK, Nickoloff J, Kulesza CA, Yasui A, Côté J, Kutateladze TG. Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1. Nat Struct Mol Biol, 2012,19(12):1266-1272. doi: 10.1038/nsmb.2435
[87]	Hassan AH, Awad S, Prochasson P. The Swi2/Snf2 bromodomain is required for the displacement of SAGA and the octamer transfer of SAGA-acetylated nucleosomes. J Biol Chem, 2006,281(26):18126-18134. doi: 10.1074/jbc.M602851200 pmid: 16648632
[88]	Johnson LM, Bostick M, Zhang XY, Kraft E, Henderson I, Callis J, Jacobsen SE. The SRA Methyl-Cytosine-Binding domain links DNA and histone methylation. Curr Biol, 2007,17(4):379-384. doi: 10.1016/j.cub.2007.01.009
[89]	Patnaik D, Esteve PO, Pradhan S. Targeting the SET and RING-associated (SRA) domain of ubiquitin-like, PHD and ring finger-containing 1 (UHRF1) for anti-cancer drug development. Oncotarget, 2018,9(40):26243-26258. doi: 10.18632/oncotarget.25425 pmid: 29899856
[90]	Liu SM, Yu Y, Ruan Y, Meyer D, Wolff M, Xu L, Wang N, Steinmetz A, Shen WH. Plant SET- and RING- associated domain proteins in heterochromatinization. The Plant Journal, 2007,52(5):914-926. doi: 10.1111/j.1365-313X.2007.03286.x pmid: 17892444
[91]	Ouyang J, Gill G. SUMO engages multiple corepressors to regulate chromatin structure and transcription. Epigenetics, 2009,4(7):440-444. doi: 10.4161/epi.4.7.9807 pmid: 19829068
[92]	Zeng L, Yap KL, Ivanov AV, Wang XQ, Mujtaba S, Plotnikova O, Rauscher Iii FJ, Zhou MM. Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat Struct Mol Biol, 2008,15(6):626-633. doi: 10.1038/nsmb.1416 pmid: 18488044
[93]	Yang ZF, Sun LP, Zhang PP, Zhang YX, Yu P, Liu L, Abbas A, Xiang XJ, Wu WX, Zhan XD, Cao LY, Cheng SH. TDR INTERACTING PROTEIN 3, encoding a PHD-finger transcription factor, regulates Ubisch bodies and pollen wall formation in rice. Plant J, 2019,99(5):844-861. doi: 10.1111/tpj.14365 pmid: 31021015
[94]	Martin C, Zhang Y. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol, 2005,6(11):838-849. doi: 10.1038/nrm1761 pmid: 16261189
[95]	Amato A, Lucas X, Bortoluzzi A, Wright D, Ciulli A. Targeting ligandable pockets on plant homeodomain (PHD) zinc finger domains by a Fragment-Based approach. Acs Chem Biol, 2018,13(4):915-921. doi: 10.1021/acschembio.7b01093 pmid: 29529862
[96]	Wagner EK, Nath N, Flemming R, Feltenberger JB, Denu JM. Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry, 2012,51(41):8293-8306. doi: 10.1021/bi3009278

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

植物PHD结构域蛋白的结构与功能特性

Structural and functional characteristics of plant PHD domain-containing proteins

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 5

参考文献 96

相关文章 15

编辑推荐

Metrics

[1]	王承贤, 容益康, 崔敏. 果蝇限制端粒转座子的分子机制[J]. 遗传, 2023, 45(3): 221-228.
[2]	吴丹丹, 朱明昆, 方忠艳, 马伟. 植物B染色体的分子结构组成及遗传机制研究进展[J]. 遗传, 2022, 44(9): 772-782.
[3]	赵岩, 王晨鑫, 杨天明, 李春爽, 张丽宏, 杜冬妮, 王若曦, 王静, 魏民, 巴雪青. DNA氧化损伤8-羟鸟嘌呤与肿瘤的发生发展[J]. 遗传, 2022, 44(6): 466-477.
[4]	张元, 赵语婷, 庄乐南, 贺津. 转录中介体复合物在心血管发育和疾病中的转录调控作用[J]. 遗传, 2022, 44(5): 383-397.
[5]	曲卉, 柳毅, 陈雅文, 汪晖. 环境因素所致印迹基因改变与子代器官发育[J]. 遗传, 2022, 44(2): 107-116.
[6]	张杨景晖, 常沛瑶, 杨紫淑, 薛宇航, 李雪奇, 张旸. 表观遗传修饰影响花青苷合成研究进展[J]. 遗传, 2022, 44(12): 1117-1127.
[7]	赵清雯, 潘东宁. 表观遗传修饰对脂肪组织产热的调控进展[J]. 遗传, 2022, 44(10): 867-880.
[8]	刘国芳, 任沛东, 叶文新, 陆光涛. 十字花科黑腐病菌中转录因子HpaR1与Clp调控一个糖苷水解酶基因表达的分析[J]. 遗传, 2021, 43(9): 910-920.
[9]	何江平, 陈捷凯. 转座元件、表观遗传调控与细胞命运决定[J]. 遗传, 2021, 43(9): 822-834.
[10]	王雅楠, 徐涛, 王万鹏, 张庆祝, 解莉楠. 表观遗传修饰在作物重要性状形成中的作用[J]. 遗传, 2021, 43(9): 858-879.
[11]	袁洁, 蔡时青. 衰老过程中行为和认知功能退化的调控机制研究[J]. 遗传, 2021, 43(6): 545-570.
[12]	张向前, 李楠, 解新明. 表观遗传学综合性实验设计与探讨[J]. 遗传, 2021, 43(12): 1179-1187.
[13]	刘国芳, 王欣欣, 苏辉昭, 陆光涛. 细菌GntR家族转录调控因子的研究进展[J]. 遗传, 2021, 43(1): 66-73.
[14]	邱晓芬, 汤冬娥, 虞海燕, 廖秋燕, 胡芷洋, 周俊, 赵鑫, 何慧燕, 梁灼健, 许承明, 杨明, 戴勇. 基于单细胞ATAC测序技术对18-三体综合征染色质开放性区域转录因子的分析[J]. 遗传, 2021, 43(1): 74-83.
[15]	胡颖楚, 胡豪畅, 林少沂, 陈晓敏. DNA羟甲基化调控动脉粥样硬化的研究进展[J]. 遗传, 2020, 42(7): 632-640.