染色质免疫共沉淀测序技术及其在园艺植物中的应用研究进展

doi:10.16420/j.issn.0513-353x.2023-0125

摘要/Abstract

摘要：

近年来，基于染色质免疫共沉淀技术（ChIP）与第二代测序技术结合的染色质免疫共沉淀测序技术（ChIP-seq）已被广泛用于研究DNA与蛋白质的相互作用，对解析园艺植物基因的表达与调控、靶基因筛选与定位、调控网络构建、染色质开放程度确认等方面具有较大的优势。本文综述了ChIP-seq技术的发展简史及其在园艺植物转录因子和组蛋白修饰中所取得的进展，以期为园艺植物DNA—蛋白互作研究提供参考。

关键词: DNA与蛋白质互作, 染色质免疫共沉淀测序, 转录因子, 组蛋白修饰

Abstract:

In recent years，chromatin immunoprecipitation sequencing technology (ChIP-seq) based on the combination of chromatin immunoprecipitation technology (ChIP) and second-generation sequencing technology has been widely used to study the interaction between DNA and proteins. It has great advantages in analyzing the expression and regulation of horticultural plant genes，screening and mapping of target genes，construction of regulatory networks，and confirmation of chromatin openness. This paper reviews the development history of ChIP-seq technology and its progress in the modification of transcription factors and histones in horticultural plants，with the aim of providing theoretical reference for the study of DNA-protein interactions in horticultural plants.

Key words: DNA and protein interaction, chromatin immunoprecipitation sequencing, transcription factor, histone modification

翟挺楷, 马湘玮, 陈燕, 张雪莹, 李卓蕴, 徐卢振, 傅卓然, 赖钟雄, 林玉玲. 染色质免疫共沉淀测序技术及其在园艺植物中的应用研究进展[J]. 园艺学报, 2024, 51(1): 39-52.

ZHAI Tingkai, MA Xiangwei, CHEN Yan, ZHANG Xueying, LI Zhuoyun, XÜ Luzhen, FU Zhuoran, LAI Zhongxiong, LIN Yuling. Advances in Chromatin Immunoprecipitation Sequencing and Its Application in Horticultural Plants[J]. Acta Horticulturae Sinica, 2024, 51(1): 39-52.

图/表 3

参考文献 72

[1]	Adli M, Bernstein B E. 2011. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc, 6 (10):1656-1668. doi: 10.1038/nprot.2011.402 pmid: 21959244
[2]	Akhtar J, More P, Albrecht S, Marini F, Kaiser W, Kulkarni A, Wojnowski L, Fontaine J F, Andrade-Navarro M A, Silies M, Berger C. 2019. TAF-ChIP:an ultra-low input approach for genome-wide chromatin immunoprecipitation assay. Life Sci Alliance, 2 (4):e201900318. doi: 10.26508/lsa.201900318 URL
[3]	An Guanghui. 2022. The genetic and molecular mechanisms of LsSAW1 regulating heading and leaf dorsiventrality in lettuce[Ph. D. Dissertation]. Wuhan: Huazhong Agricultural University. (in Chinese)
	安光辉. 2022. LsSAW1调控生菜结球及叶背腹性的遗传和分子机理[博士论文]. 武汉: 华中农业大学.
[4]	Bartosovic M, Kabbe M, Castelo-Branco G. 2021. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat Biotechnol, 39 (7):825-835. doi: 10.1038/s41587-021-00869-9 pmid: 33846645
[5]	Bernstein B E, Humphrey E L, Erlich R L, Schneider R, Bouman P, Liu J S, Kouzarides T, Schreiber S L. 2002. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci USA, 99 (13):8695-8700. doi: 10.1073/pnas.082249499 pmid: 12060701
[6]	Boersma M R, Patrick R M, Jillings S L, Shaipulah N, Sun P, Haring M A, Dudareva N, Li Y, Schuurink R C. 2022. ODORANT 1 targets multiple metabolic networks in petunia flowers. Plant J, 109 (5):1134-1151. doi: 10.1111/tpj.v109.5 URL
[7]	Brind’Amour J, Liu S, Hudson M, Chen C, Karimi M M, Lorincz M C. 2015. An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat Commun, 6:6033. doi: 10.1038/ncomms7033 pmid: 25607992
[8]	Canton M, Forestan C, Marconi G, Carrera E, Bonghi C, Varotto S. 2022. Evidence of chromatin and transcriptional dynamics for cold development in peach flower bud. New Phytol, 236 (3):974-988. doi: 10.1111/nph.18393 pmid: 35860865
[9]	Chen P, Yan M, Li L, He J, Zhou S, Li Z, Niu C, Bao C, Zhi F, Ma F, Guan Q. 2020. The apple DNA-binding one zinc-finger protein MdDof 54 promotes drought resistance. Hortic Res, 7 (1):195. doi: 10.1038/s41438-020-00419-5
[10]	Chen P, Zhi F, Li X, Shen W, Yan M, He J, Bao C, Fan T, Zhou S, Ma F, Guan Q. 2022. Zinc-finger protein MdBBX7/MdCOL9,a target of MdMIEL 1 E3 ligase,confers drought tolerance in apple. Plant Physiol, 188 (1):540-559. doi: 10.1093/plphys/kiab420 URL
[11]	Chen Y, Dan Z, Gao F, Chen P, Fan F, Li S. 2020. Rice GROWTH-REGULATING FACTOR7 Modulates plant architecture through regulating GA and Indole-3-Acetic Acid metabolism. Plant Physiol, 184 (1):393-406. doi: 10.1104/pp.20.00302 URL
[12]	Chen Y, Ma X, Xue X, Liu M, Zhang X, Xiao X, Lai C, Zhang Z, Lai Z, Lin Y. 2023. Genome-wide analysis of the SAUR gene family and function exploration of DlSAUR32 during early longan somatic embryogenesis. Plant Physiol Biochem, 195:362-374. doi: 10.1016/j.plaphy.2023.01.006 URL
[13]	Ding X, Liu X, Jiang G, Li Z, Song Y, Zhang D, Jiang Y, Duan X. 2022. SlJMJ 7 orchestrates tomato fruit ripening via crosstalk between H3K4me3 and DML2-mediated DNA demethylation. New Phytol, 233 (3):1202-1219. doi: 10.1111/nph.v233.3 URL
[14]	Dou Wanfu. 2020. Molecular mechanism of the transeription factor CsBZIP40 enhancing resistance to citrus bacterial canker disease[M. D. Dissertation]. Chongqing: Southwest University. (in Chinese)
	窦万福. 2020. 转录因子CsBZIP40增强柑橘对溃疡病抗性的分子机制解析[硕士论文]. 重庆: 西南大学.
[15]	Du M, Zhao J, Tzeng D, Liu Y, Deng L, Yang T, Zhai Q, Wu F, Huang Z, Zhou M, Wang Q, Chen Q, Zhong S, Li C B, Li C. 2017. MYC 2 Orchestrates a hierarchical transcriptional cascade that regulates jasmonate-mediated plant immunity in tomato. Plant Cell, 29 (8):1883-1906. doi: 10.1105/tpc.16.00953 URL
[16]	Feng Yanchun. 2019. Analysis of expression characteristics of tomato SNAC4/9 proteins and regulatiion of target genes[M. D. Dissertation].. Tianjin: Tianjin University. (in Chinese)
	冯炎春. 2019. 番茄SNAC4/9蛋白的表达特性分析及调控的靶基因研究[硕士论文]. 天津: 天津大学.
[17]	Gao Guori, Zhang T, Chen D, He C. 2018. Genome-wide analysis of H3K9ac in Hippophae rhamnoides. Journal of Northwestern Botany, 38 (2):242-248. (in Chinese)
	高国日, 张彤, 陈道国, 何彩云. 2018. 沙棘H3K9ac乙酰化修饰全基因组分析. 西北植物学报, 38 (2):242-248.
[18]	Geng D, Chen P, Shen X, Zhang Y, Li X, Jiang L, Xie Y, Niu C, Zhang J, Huang X, Ma F, Guan Q. 2018. MdMYB88 and MdMYB 124 enhance drought tolerance by modulating root vessels and cell walls in apple. Plant Physiol, 178 (3):1296-1309. doi: 10.1104/pp.18.00502 URL
[19]	Gilmour D S, Lis J T. 1984. Detecting protein-DNA interactions in vivo:distribution of RNA polymerase on specific bacterial genes. Proc Natl Acad Sci USA, 81 (14):4275-4279. pmid: 6379641
[20]	Hainer S J, Boskovic A, McCannell K N, Rando O J, Fazzio T G. 2019. Profiling of pluripotency factors in single cells and early embryos. Cell, 177 (5):1319-1329. doi: S0092-8674(19)30276-4 pmid: 30955888
[21]	Han Y, Lu M, Yue S, Li K, Dong M, Liu L, Wang H, Shang F. 2022. Comparative methylomics and chromatin accessibility analysis in Osmanthus fragrans uncovers regulation of genic transcription and mechanisms of key floral scent production. Hortic Res, 9:c96.
[22]	He K, Feng Y, An S, Liu F, Xiang G. 2022. Integrative epigenomic profiling reveal AP-1 is a key regulator in intrahepatich cholangiocarcinoma. Genomics, 114 (1):241-252. doi: 10.1016/j.ygeno.2021.12.008 URL
[23]	He Q, Johnston J, Zeitlinger J. 2015. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat Biotechnol, 33 (4):395-401. doi: 10.1038/nbt.3121
[24]	Hu Y N, Sun H L, Han Z Y, Wang S, Wang T, Li Q Q, Tian J, Wang Y, Zhang X Z, Xu X F, Han Z H, Wu T. 2022. ERF4 affects fruit ripening by acting as a JAZ interactor between ethylene and jasmonic acid hormone signaling pathways. Horticultural Plant Journal, 8 (6):689-699. doi: 10.1016/j.hpj.2022.01.002 URL
[25]	Huang Xiaorong. 2019. The possible regulatory mechanism of H3K27me3 during the ripening of Fragaria vesca[M. D. Dissertation]. Nanjing: Nanjing Agricultural University. (in Chinese)
	黄晓荣. 2019. H3K27me3在草莓成熟过程中的调控机理探讨[硕士论文]. 南京: 南京农业大学.
[26]	Iqbal S, Pan Z, Wu X, Shi T, Ni X, Bai Y, Gao J, Khalil-Ur-Rehman M, Gao Z. 2020. Genome-wide analysis of PmTCP 4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot. Plant Genome, 13 (3):e20052. doi: 10.1002/tpg2.v13.3 URL
[27]	Johnson D S, Mortazavi A, Myers R M, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science, 316 (5830):1497-1502. doi: 10.1126/science.1141319 pmid: 17540862
[28]	Kasinathan S, Orsi G A, Zentner G E, Ahmad K, Henikoff S. 2014. High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods, 11 (2):203-209. doi: 10.1038/nmeth.2766 pmid: 24336359
[29]	Kaya-Okur H S, Wu S J, Codomo C A, Pledger E S, Bryson T D, Henikoff J G, Ahmad K, Henikoff S. 2019. CUT & Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun, 10 (1):1930. doi: 10.1038/s41467-019-09982-5 pmid: 31036827
[30]	Klasfeld S, Roule T, Wagner D. 2022. Greenscreen:a simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data. Plant Cell, 34 (12):4795-4815. doi: 10.1093/plcell/koac282 URL
[31]	Kowar T, Zakrzewski F, Macas J, Koblizkova A, Viehoever P, Weisshaar B, Schmidt T. 2016. Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris). BMC Plant Biol, 16 (1):120. doi: 10.1186/s12870-016-0805-5 pmid: 27230558
[32]	Kuang J F, Chen J Y, Liu X C, Han Y C, Xiao Y Y, Shan W, Tang Y, Wu K Q, He J X, Lu W J. 2017. The transcriptional regulatory network mediated by banana (Musa acuminata) dehydration-responsive element binding (MaDREB) transcription factors in fruit ripening. New Phytol, 214 (2):762-781. doi: 10.1111/nph.2017.214.issue-2 URL
[33]	Li Z, Jiang G, Liu X, Ding X, Zhang D, Wang X, Zhou Y, Yan H, Li T, Wu K, Jiang Y, Duan X. 2020. Histone demethylase SlJMJ 6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato. New Phytol, 227 (4):1138-1156. doi: 10.1111/nph.v227.4 URL
[34]	Lin Ying. 2020. Co-evolution of HP1s,HKMTases and HDMases and theiridentification and expression patterns in Fragaria[M. D. Dissertation]. Nanjing: Nanjing Agricultural University. (in Chinese)
	林莹. 2020. HP1和组蛋白甲基修饰酶的共进化及其在草莓中的鉴定和表达模式分析[硕士论文]. 南京: 南京农业大学.
[35]	Liu Y, Shi Y, Zhu N, Zhong S, Bouzayen M, Li Z. 2020. SlGRAS 4 mediates a novel regulatory pathway promoting chilling tolerance in tomato. Plant Biotechnol J, 18 (7):1620-1633. doi: 10.1111/pbi.v18.7 URL
[36]	Liu Z, Li Z, Wu S, Yu C, Wang X, Wang Y, Peng Z, Gao Y, Li R, Shen Y, Duan L. 2022. Coronatine enhances chilling tolerance of tomato plants by inducing chilling-related epigenetic adaptations and transcriptional reprogramming. Int J Mol Sci, 23 (17):10049. doi: 10.3390/ijms231710049 URL
[37]	Ma X, Chen Y, Liu M, Xue X, Zhang X, Xu L, Lai Z, Lin Y. 2022. Genome-wide analysis of the XTH gene family and functional analysis of DlXTH23.5/25 during early longan somatic embryogenesis. Front Plant Sci, 13:1043464. doi: 10.3389/fpls.2022.1043464 URL
[38]	Nishikori S, Hattori T, Fuchs S M, Yasui N, Wojcik J, Koide A, Strahl B D, Koide S. 2012. Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. J Mol Biol, 424 (5):391-399. doi: 10.1016/j.jmb.2012.09.022 pmid: 23041298
[39]	Nishio H, Nagano A J, Ito T, Suzuki Y, Kudoh H. 2020. Seasonal plasticity and diel stability of H3K27me 3 in natural fluctuating environments. Nat Plants, 6 (9):1091-1097. doi: 10.1038/s41477-020-00757-1
[40]	O’Neill L P, Turner B M. 2003. Immunoprecipitation of native chromatin:NChIP. Methods, 31 (1):76-82. doi: 10.1016/S1046-2023(03)00090-2 URL
[41]	Poza-Viejo L, Paya-Milans M, San M P, Castro-Labrador L, Lara-Astiaso D, Wilkinson M D, Pineiro M, Jarillo J A, Crevillen P. 2022. Conserved and distinct roles of H3K27me 3 demethylases regulating flowering time in Brassica rapa. Plant Cell Environ, 45 (5):1428-1441. doi: 10.1111/pce.v45.5 URL
[42]	Rhee H S, Pugh B F. 2011. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell, 147 (6):1408-1419. doi: 10.1016/j.cell.2011.11.013 pmid: 22153082
[43]	Rhee H S, Pugh B F. 2012. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature, 483 (7389):295-301. doi: 10.1038/nature10799
[44]	Ricardi M M, Gonzalez R M, Zhong S, Dominguez P G, Duffy T, Turjanski P G, Salgado S J, Alleva K, Carrari F, Giovannoni J J, Estevez J M, Iusem N D. 2014. Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1,a drought stress-responsive transcription factor. BMC Plant Biol, 14:29. doi: 10.1186/1471-2229-14-29
[45]	Rotem A, Ram O, Shoresh N, Sperling R A, Goren A, Weitz D A, Bernstein B E. 2015. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol, 33 (11):1165-1172. doi: 10.1038/nbt.3383 pmid: 26458175
[46]	Salehin N, Santucci N, Osteil P, Tam P. 2022. Exploring chromatin accessibility in mouse epiblast stem cells with ATAC-Seq. Methods Mol Biol, 2490:93-100. doi: 10.1007/978-1-0716-2281-0_9 pmid: 35486242
[47]	Schwope R, Magris G, Miculan M, Paparelli E, Celii M, Tocci A, Marroni F, Fornasiero A, de Paoli E, Morgante M. 2021. Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. Plant J, 107 (6):1631-1647. doi: 10.1111/tpj.v107.6 URL
[48]	Skene P J, Henikoff S. 2017. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife, 6:e21856. doi: 10.7554/eLife.21856 URL
[49]	Solomon M J, Varshavsky A. 1985. Formaldehyde-mediated DNA-protein crosslinking:a probe for in vivo chromatin structures. Proc Natl Acad Sci USA, 82 (19):6470-6474. pmid: 2995966
[50]	Tu Mingxing. 2021. Drought resistance function and regulation mechanism analysis of grapevine transcription factor VIbZIP30 gene[Ph. D. Dissertation]. Yangling: Northwest A & F University. (in Chinese)
	涂明星. 2021. 葡萄转录因子VlbZIP30抗旱功能及其调控机理研究[博士论文]. 杨凌: 西北农林科技大学.
[51]	Visel A, Blow M J, Li Z, Zhang T, Akiyama J A, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin E M, Pennacchio L A. 2009. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature, 457 (7231):854-858. doi: 10.1038/nature07730
[52]	Wang Q, Xiong H, Ai S, Yu X, Liu Y, Zhang J, He A. 2019. CoBATCH for high-throughput single-cell epigenomic profiling. Mol Cell, 76 (1):206-216. doi: S1097-2765(19)30545-3 pmid: 31471188
[53]	Wang Xiaotian. 2021. Map-based cloning and functional analysis of qMIB1,an inflorescence branching number regulator in tomato[Ph. D. Dissertation]. Beijing: Chinese Academy of Agricultural Sciences. (in Chinese)
	王晓甜. 2021. 番茄花序分枝调控基因qMIB1的图位克隆及功能分析[博士论文]. 北京: 中国农业科学院.
[54]	Wu Qiong. 2019. Study of ABA-ethylene interaction on theregulation of cherry tomato fruit ripening[Ph. D. Dissertation]. Hangzhou: Zhejiang University. (in Chinese)
	吴琼. 2019. ABA-乙烯互作调控樱桃番茄果实成熟的效应与机理研究[博士论文]. 杭州: 浙江大学.
[55]	Wu R, Wang T, Warren B, Thomson S J, Allan A C, Macknight R C, Varkonyi-Gasic E. 2018. Kiwifruit SVP 2 controls developmental and drought-stress pathways. Plant Mol Biol, 96 (3):233-244. doi: 10.1007/s11103-017-0688-3 URL
[56]	Xiao X, Lin W, Feng E, Wu C, Ou X. 2022. Genome-wide identification of binding sites for SmTCP7a transcription factors of eggplant during bacterial wilt resistance by ChIP-Seq. Int J Mol Sci, 23 (12):6844. doi: 10.3390/ijms23126844 URL
[57]	Xie Y, Chen P, Yan Y, Bao C, Li X, Wang L, Shen X, Li H, Liu X, Niu C, Zhu C, Fang N, Shao Y, Zhao T, Yu J, Zhu J, Xu L, van Nocker S, Ma F, Guan Q. 2018. An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple. New Phytol, 218 (1):201-218. doi: 10.1111/nph.14952 pmid: 29266327
[58]	Xu Mengnan. 2015. Preliminary investigation of mechanism of TCP gene regulating the development of cucumber tendrils[M. D. Dissertation]. Beijing: Chinese Academy of Agricultural Sciences. (in Chinese)
	许梦楠. 2015. TCP基因调控黄瓜卷须发育机理的初探[硕士论文]. 北京: 中国农业科学院.
[59]	Yan F, Gao Y, Pang X, Xu X, Zhu N, Chan H, Hu G, Wu M, Yuan Y, Li H, Zhong S, Hada W, Deng W, Li Z. 2020. BEL1-LIKE HOMEODOMAIN4 regulates chlorophyll accumulation,chloroplast development,and cell wall metabolism in tomato fruit. J Exp Bot, 71 (18):5549-5561. doi: 10.1093/jxb/eraa272 URL
[60]	Yang Feng. 2021. Establishment and application of dual cut CRISPR/Cas9 gene editing and ChIP-Seq system in pear calli[M. D. Dissertation]. Hangzhou: Zhejiang University. (in Chinese)
	杨锋. 2021. 基于梨愈伤组织的CRISPR/Cas9基因编辑系统和ChIP-Seq体系的建立与应用[硕士论文]. 杭州: 浙江大学.
[61]	Yu Qinhan. 2022. Response mechanism of Amur grape VaMYB4a in response to cold stress[M. D. Dissertation]. Yinchuan: Ningxia University. (in Chinese)
	俞沁含. 2022. 山葡萄VaMYB4a参与低温胁迫应答的机理研究[硕士论文]. 银川: 宁夏大学.
[62]	Yu Qinhan, Li Junduo, Cui Ying, Wang Jiahui, Zheng Qiaoling, Xu Weirong. 2023. Screening and identification of interacting protein of VaMYB4a from Vitis amurensis. Acta Horticulturae Sinica, 50 (3):508-522. (in Chinese) doi: 10.16420/j.issn.0513-353x.2021-1219 URL
	俞沁含, 李俊铎, 崔莹, 王佳慧, 郑巧玲, 徐伟荣. 2023. 山葡萄转录因子VaMYB4a互作蛋白的筛选与鉴定. 园艺学报, 50 (3):508-522. doi: 10.16420/j.issn.0513-353x.2021-1219 URL
[63]	Zhang H, Cheng F, Xiao Y, Kang X, Wang X, Kuang R, Ni M. 2017. Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development. Plant J, 91 (1):158-171. doi: 10.1111/tpj.2017.91.issue-1 URL
[64]	Zhang Q, Guan P, Zhao L, Ma M, Xie L, Li Y, Zheng R, Ouyang W, Wang S, Li H, Zhang Y, Peng Y, Cao Z, Zhang W, Xiao Q, Xiao Y, Fu T, Li G, Li X, Shen J. 2021. Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus. Mol Plant, 14 (4):604-619. doi: 10.1016/j.molp.2020.12.020 pmid: 33387675
[65]	Zhang Qing. 2021. Study of epigenome maps and subgenome imbalance in Brassica napus[Ph. D. Dissertation]. Wuhan: Huazhong Agricultural University. (in Chinese)
	章清. 2021. 甘蓝型油菜表观遗传图谱和亚基因组不平衡的研究[博士论文]. 武汉: 华中农业大学.
[66]	Zhang X, Xu X, Han Z, Wu T. 2022. ERF 4 affects fruit ripening by acting as a JAZ interactor between ethylene and jasmonic acid hormone signaling pathways. Horticultural Plant Journal, 8 (6):689-699. doi: 10.1016/j.hpj.2022.01.002 URL
[67]	Zhang Zhen. 2019. Identification and functional analysis of SF2 in controlling of fruit length in Cucumis sativus L. [Ph. D. Dissertation]. Yangling: Northwest A & F University. (in Chinese)
	张震. 2019. 黄瓜果实长度调控基因SF2的克隆及分子机制的研究[博士论文]. 杨凌: 西北农林科技大学.
[68]	Zhou M, Palanca A, Law J A. 2018. Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family. Nat Genet, 50 (6):865-873. doi: 10.1038/s41588-018-0115-y
[69]	Zhu B, Hsieh Y P, Murphy T W, Zhang Q, Naler L B, Lu C. 2019. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc, 14 (12):3366-3394. doi: 10.1038/s41596-019-0223-x pmid: 31666743
[70]	Zhu Z F, Li Q Y, Gichuki D K, Hou Y J, Liu Y S, Zhou H M, Xu C, Fang L C, Gong L Z, Zheng B B, Duan W, Fan P G, Wang Q F, Xin H P. 2023. Genome-wide profiling of histone H3 lysine 27 trimethylation and its modification in response to chilling stress in grapevine leaves. Horticultural Plant Journal, 9 (3):496-508. doi: 10.1016/j.hpj.2023.03.002 URL
[71]	Zhu Zhixuan. 2015. Studies on NnCenH3 protein and centromeric DNA of sacred lotus(Nelumbo nucifera Gaertn.)[Ph. D. Dissertation]. Wuhan: Wuhan University. (in Chinese)
	朱之轩. 2015. 莲藕(Nelumbo nucifera Gaertn.)着丝粒蛋白NnCenH3和着丝粒DNA序列研究[博士论文]. 武汉: 武汉大学.
[72]	Zou X, Du M, Liu Y, Wu L, Xu L, Long Q, Peng A, He Y, Andrade M, Chen S. 2021. CsLOB 1 regulates susceptibility to citrus canker through promoting cell proliferation in citrus. Plant J, 106 (4):1039-1057. doi: 10.1111/tpj.v106.4 URL

发展阶段 Stage	技术名称 Technical name	细胞数 Number of cell	新/优化技术 New/optimization technology	优点 Advantage	缺点 Disadvantage	细胞/组织水平Cell/ tissue level	参考文献 Reference
初期 Initial （1984— 2010）	ChIP	10⁷	新技术 New technology	有利于富集与蛋白相结合的DNA片段It’s good for enriching DNA fragments that bind to proteins	交联效果差；样本需求量大Formaldehyde crosslinking effect is poor；High demand for samples	组织 Tissue	Gilmour & Lis,1984
	ChIP-chip	10⁷	新技术 New technology	基因组微阵列技术对DNA定位Genomic microarray technique for DNA localization	试验重复性低 Low test repeatability	组织 Tissue	Bernstein et al.,2002
	ChIP-seq	10⁷	新技术 New technology	转录因子结合位点与组蛋白修饰区域定位Localization of transcription factor binding sites and histone modification regions	样本需求量大；试验重复性低；易出现假阳性 Large sample demand; Low test repeatability; Prone to false positives	组织 Tissue	Johnson et al.,2007
探索发展 Explorative （2011— 2018）	ChIP-exo	10⁶	优化：酶切 Optimization：MNase cutting	降低测序假阳性；提高单bp准确性Reduce false positive sequencing results; Improve the accuracy of single bp	样本需求量大；对技术要求高Large sample demand; High technical requirements	组织 Tissue	Rhee & Pugh,2011
	Nano- ChIP-seq	10⁴	优化：文库构建 Optimization：library construction	抑制DNA中GC含量；降低样本需求量Inhibition of GC content in DNA; Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Adli & Bernstein,2011
	scChIP-seq	单细胞 Single cell	新技术 New technology	高度集成化；实现单细胞测序Highly integrated; Single cell sequencing was realized	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Rotem et al.,2015
	ChIP-nexus	10⁶	优化：文库构建 Optimization： library construction	降低文库构建的DNA需求量Reduce the DNA requirement for library construction	样本需求量大 Large sample demand	组织 Tissue	He et al.,2015
	ULI- NChIP	10³	优化：细胞分离 Optimization：cell separation	降低样本需求量；无需甲醛交联Lower the quantity of samples；No formaldehyde crosslinking required	ChIP时损失DNA影响测序准确性DNA loss during ChIP affects the accuracy of subsequent sequencing results	组织 Tissue	Brind’ Amour et al.,2015
	CUT&RUN	10² ~ 10³	新技术 New technology	富集和染色质片段化同时进行；省去ChIP；降低背景噪音Enrichment occurs simultaneously with chromatin fragmentation; Omit ChIP; Reduce background noise	易发生DNA损失 Prone to DNA loss	组织 Tissue	Skene & Henikoff,2017
快速发展 Rapid （2019—）	ULI-CUT& RUN	10 ~ 10²	优化： CUT&RUN Optimization：CUT&RUN	采用流式细胞分选实现极少数细胞测序Very few cells were sequenced by flow cytometry	易发生DNA损失 Prone to DNA loss	组织 Tissue	Hainer et al.,2019
	CUT&Tag	10²~ 10³	新技术 New technology	靶向切割产物可以直接进行文库扩增 Targeted cleavage products can be directly amplified into the library	易出现假阳性 Prone to false positives	组织 Tissue	Kaya-Okur et al.,2019
	TAF-ChIP	10²	优化：细胞分离 Optimization：cell separation	无需DNA纯化与文库构建；降低对样本需求量No DNA purification and library construction；Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Akhtar et al.,2019
	MOW ChIP-seq	10² ~ 10⁴	优化：免疫共沉Optimization：ChIP	降低对试剂消耗；便于自动化 Reduce the consumption of reagents; Facilitate automation	对技术要求高High technical requirements	组织 Tissue	Zhu et al.,2019
快速发展 Rapid （2019—）	CoBATCH	10⁴	新技术 New technology	实现不同样本高通量单细胞测序Achieve high throughput single cell sequencing of different samples	无法直接在单细胞水平进行分析Samples cannot be analyzed directly at the single-cell level	组织 Tissue	Wang et al.,2019
	scCUT&Tag	单细胞 Single cell	优化：CUT&Tag Optimization： CUT&Tag	单细胞水平测序；高信噪比 Single-cell level sequencing; High signal-to-noise ratio	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Bartosovic et al.,2021
	Greenscreen	10⁷	新技术 New technology	提高样本间可重复性；消除假阳性Improve repeatability between samples; Eliminate false positives	对数据处理技术要求高 High requirements on data processing technology	组织 Tissue	Klasfeld et al.,2022

发展阶段 Stage	技术名称 Technical name	细胞数 Number of cell	新/优化技术 New/optimization technology	优点 Advantage	缺点 Disadvantage	细胞/组织水平Cell/ tissue level	参考文献 Reference
初期 Initial （1984— 2010）	ChIP	10⁷	新技术 New technology	有利于富集与蛋白相结合的DNA片段It’s good for enriching DNA fragments that bind to proteins	交联效果差；样本需求量大Formaldehyde crosslinking effect is poor；High demand for samples	组织 Tissue	Gilmour & Lis,1984
	ChIP-chip	10⁷	新技术 New technology	基因组微阵列技术对DNA定位Genomic microarray technique for DNA localization	试验重复性低 Low test repeatability	组织 Tissue	Bernstein et al.,2002
	ChIP-seq	10⁷	新技术 New technology	转录因子结合位点与组蛋白修饰区域定位Localization of transcription factor binding sites and histone modification regions	样本需求量大；试验重复性低；易出现假阳性 Large sample demand; Low test repeatability; Prone to false positives	组织 Tissue	Johnson et al.,2007
探索发展 Explorative （2011— 2018）	ChIP-exo	10⁶	优化：酶切 Optimization：MNase cutting	降低测序假阳性；提高单bp准确性Reduce false positive sequencing results; Improve the accuracy of single bp	样本需求量大；对技术要求高Large sample demand; High technical requirements	组织 Tissue	Rhee & Pugh,2011
	Nano- ChIP-seq	10⁴	优化：文库构建 Optimization：library construction	抑制DNA中GC含量；降低样本需求量Inhibition of GC content in DNA; Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Adli & Bernstein,2011
	scChIP-seq	单细胞 Single cell	新技术 New technology	高度集成化；实现单细胞测序Highly integrated; Single cell sequencing was realized	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Rotem et al.,2015
	ChIP-nexus	10⁶	优化：文库构建 Optimization： library construction	降低文库构建的DNA需求量Reduce the DNA requirement for library construction	样本需求量大 Large sample demand	组织 Tissue	He et al.,2015
	ULI- NChIP	10³	优化：细胞分离 Optimization：cell separation	降低样本需求量；无需甲醛交联Lower the quantity of samples；No formaldehyde crosslinking required	ChIP时损失DNA影响测序准确性DNA loss during ChIP affects the accuracy of subsequent sequencing results	组织 Tissue	Brind’ Amour et al.,2015
	CUT&RUN	10² ~ 10³	新技术 New technology	富集和染色质片段化同时进行；省去ChIP；降低背景噪音Enrichment occurs simultaneously with chromatin fragmentation; Omit ChIP; Reduce background noise	易发生DNA损失 Prone to DNA loss	组织 Tissue	Skene & Henikoff,2017
快速发展 Rapid （2019—）	ULI-CUT& RUN	10 ~ 10²	优化： CUT&RUN Optimization：CUT&RUN	采用流式细胞分选实现极少数细胞测序Very few cells were sequenced by flow cytometry	易发生DNA损失 Prone to DNA loss	组织 Tissue	Hainer et al.,2019
	CUT&Tag	10²~ 10³	新技术 New technology	靶向切割产物可以直接进行文库扩增 Targeted cleavage products can be directly amplified into the library	易出现假阳性 Prone to false positives	组织 Tissue	Kaya-Okur et al.,2019
	TAF-ChIP	10²	优化：细胞分离 Optimization：cell separation	无需DNA纯化与文库构建；降低对样本需求量No DNA purification and library construction；Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Akhtar et al.,2019
	MOW ChIP-seq	10² ~ 10⁴	优化：免疫共沉Optimization：ChIP	降低对试剂消耗；便于自动化 Reduce the consumption of reagents; Facilitate automation	对技术要求高High technical requirements	组织 Tissue	Zhu et al.,2019
快速发展 Rapid （2019—）	CoBATCH	10⁴	新技术 New technology	实现不同样本高通量单细胞测序Achieve high throughput single cell sequencing of different samples	无法直接在单细胞水平进行分析Samples cannot be analyzed directly at the single-cell level	组织 Tissue	Wang et al.,2019
	scCUT&Tag	单细胞 Single cell	优化：CUT&Tag Optimization： CUT&Tag	单细胞水平测序；高信噪比 Single-cell level sequencing; High signal-to-noise ratio	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Bartosovic et al.,2021
	Greenscreen	10⁷	新技术 New technology	提高样本间可重复性；消除假阳性Improve repeatability between samples; Eliminate false positives	对数据处理技术要求高 High requirements on data processing technology	组织 Tissue	Klasfeld et al.,2022

物种 Species	样品 Sample	方法 Method	应用方向 Application direction	定位基因/定位组蛋白 Localization gene/ histone	参考文献 Reference
龙眼 Dimocarpus longan	胚性愈伤组织 Embryonic callus	X-ChIP	组蛋白修饰 Histone modification	H3K4me1	Ma et al.,2022；Chen et al.,2023
葡萄Vitis vinifera L.	叶片Leaf	X-ChIP	转录因子Transcription factor	VlbZIP30	涂明星,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me1、H3K4me3、 H3K27ac	Schwope et al.,2021
	叶片Leaf	X-ChIP	转录因子Transcription factor	VaMYB4a	俞沁含,2022；俞沁含等,2023
柑橘Citrus reticulata	叶片Leaf	X-ChIP	转录因子Transcription factor	CsbZIP40	窦万福,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	CsLOB1	Zou et al.,2021
苹果Malus × domestica	叶片Leaf	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Xie et al.,2018
	根系Root	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Geng et al.,2018
	叶片Leaf	X-ChIP	转录因子Transcription factor	MdDof54	Chen et al.,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	B-BOX 7/CONSTANS-LIKE 9 (MdBBX7/MdCOL9)	Chen et al.,2022
	果实Fruit	X-ChIP	转录因子Transcription factor	MdERF4	Hu et al.,2022；Zhang et al.,2022
桃Amygdalus persica	花蕾Flower bud	X-ChIP	组蛋白修饰Histone modification	H3K4me3、H3K27me3	Canton et al.,2022
杏Prunus	花蕾Flower bud	X-ChIP	转录因子Transcription factor	PmTCP4	Iqbal et al.,2020
猕猴桃Actinidia	叶片Leaf	X-ChIP	转录因子Transcription factor	SHORT VEGETATIVE PHASE (SVP2)	Wu et al.,2018
香蕉Musa nana	果实Fruit	X-ChIP	转录因子Transcription factor	Dehydration-responsive element binding (MaDREB)	Kuang et al.,2017
梨Pyrus communis	愈伤组织Callus	X-ChIP	转录因子Transcription factor	PpDAM2、PpDAM3、 PpDAM4	杨锋,2021
沙棘 Hippophae rhamnoides	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K9ac	高国日等,2018
草莓Fragaria ananassa	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K27me3	黄晓荣,2019
	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K9me2、H3K27me3	林莹,2020
黄瓜Cucumis sativus	卷须Tendril	X-ChIP	转录因子Transcription factor	TCP（TEN）	许梦楠,2015
	果实Fruit	X-ChIP	组蛋白修饰Histone modification	HDAC（SF2）	张震,2019
油菜Brassica napus	种子Seed	X-ChIP	转录因子Transcription factor	SHORT HYPOCOTYL UNDER BLUE1 (SHB1)	Zhang et al.,2017
	叶、根、花芽、角果 Leaf，root，flower bud，horn fruit	X-ChIP	组蛋白修饰 Histone modification	H3K4me1、H3K27me3	Zhang et al.,2021
	叶片Leaf	eChIP	组蛋白修饰Histone modification	H3K4me1、H3K27me3	章清,2021
番茄	叶片Leaf	X-ChIP	转录因子Transcription factor	SlMYC2	Du et al.,2017
Solanum lycopersicum	果实Fruit	X-ChIP	转录因子Transcription factor	Constans-like4 (SlCOL4)	吴琼,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	SNAC4-9	冯炎春,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	BEL1-LIKE HOMEODOMAIN4（SlBL4）	Yan et al.,2020
	果实Fruit	X-ChIP	转录因子Transcription factor	SlGRAS4	Liu et al.,2020
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K27me3	Li et al.,2020
	花序原基 Inflorescence primordium	X-ChIP	转录因子 Transcription factor	SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)、 SISTER OF TM3 (STM3)	王晓甜,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Liu et al.,2022
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Ding et al.,2022
莲藕Nelumbo nucifera	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	NnCenH3	朱之轩,2015
莴苣 Lactuca sativa var. ramosa	叶片Leaf	X-ChIP	转录因子Transcription factor	LsSAW1	安光辉,2022
茄子Solanum melongena	根系Root	X-ChIP	转录因子Transcription factor	SmTCP7a	Xiao et al.,2022
甜菜Beta vulgaris	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K9me2	Kowar et al.,2016
白菜Brassica rapa var. glabra	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K27me3	Poza-Viejo et al.,2022
桂花Osmanthus fragrans	花瓣Petal	X-ChIP	转录因子Transcription factor	COfCCD1、OfCCD4	Han et al.,2022
矮牵牛Pharbitis nil	花冠Corolla	X-ChIP	转录因子Transcription factor	ODORANT 1 (ODO1)	Boersma et al.,2022

物种 Species	样品 Sample	方法 Method	应用方向 Application direction	定位基因/定位组蛋白 Localization gene/ histone	参考文献 Reference
龙眼 Dimocarpus longan	胚性愈伤组织 Embryonic callus	X-ChIP	组蛋白修饰 Histone modification	H3K4me1	Ma et al.,2022；Chen et al.,2023
葡萄Vitis vinifera L.	叶片Leaf	X-ChIP	转录因子Transcription factor	VlbZIP30	涂明星,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me1、H3K4me3、 H3K27ac	Schwope et al.,2021
	叶片Leaf	X-ChIP	转录因子Transcription factor	VaMYB4a	俞沁含,2022；俞沁含等,2023
柑橘Citrus reticulata	叶片Leaf	X-ChIP	转录因子Transcription factor	CsbZIP40	窦万福,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	CsLOB1	Zou et al.,2021
苹果Malus × domestica	叶片Leaf	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Xie et al.,2018
	根系Root	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Geng et al.,2018
	叶片Leaf	X-ChIP	转录因子Transcription factor	MdDof54	Chen et al.,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	B-BOX 7/CONSTANS-LIKE 9 (MdBBX7/MdCOL9)	Chen et al.,2022
	果实Fruit	X-ChIP	转录因子Transcription factor	MdERF4	Hu et al.,2022；Zhang et al.,2022
桃Amygdalus persica	花蕾Flower bud	X-ChIP	组蛋白修饰Histone modification	H3K4me3、H3K27me3	Canton et al.,2022
杏Prunus	花蕾Flower bud	X-ChIP	转录因子Transcription factor	PmTCP4	Iqbal et al.,2020
猕猴桃Actinidia	叶片Leaf	X-ChIP	转录因子Transcription factor	SHORT VEGETATIVE PHASE (SVP2)	Wu et al.,2018
香蕉Musa nana	果实Fruit	X-ChIP	转录因子Transcription factor	Dehydration-responsive element binding (MaDREB)	Kuang et al.,2017
梨Pyrus communis	愈伤组织Callus	X-ChIP	转录因子Transcription factor	PpDAM2、PpDAM3、 PpDAM4	杨锋,2021
沙棘 Hippophae rhamnoides	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K9ac	高国日等,2018
草莓Fragaria ananassa	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K27me3	黄晓荣,2019
	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K9me2、H3K27me3	林莹,2020
黄瓜Cucumis sativus	卷须Tendril	X-ChIP	转录因子Transcription factor	TCP（TEN）	许梦楠,2015
	果实Fruit	X-ChIP	组蛋白修饰Histone modification	HDAC（SF2）	张震,2019
油菜Brassica napus	种子Seed	X-ChIP	转录因子Transcription factor	SHORT HYPOCOTYL UNDER BLUE1 (SHB1)	Zhang et al.,2017
	叶、根、花芽、角果 Leaf，root，flower bud，horn fruit	X-ChIP	组蛋白修饰 Histone modification	H3K4me1、H3K27me3	Zhang et al.,2021
	叶片Leaf	eChIP	组蛋白修饰Histone modification	H3K4me1、H3K27me3	章清,2021
番茄	叶片Leaf	X-ChIP	转录因子Transcription factor	SlMYC2	Du et al.,2017
Solanum lycopersicum	果实Fruit	X-ChIP	转录因子Transcription factor	Constans-like4 (SlCOL4)	吴琼,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	SNAC4-9	冯炎春,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	BEL1-LIKE HOMEODOMAIN4（SlBL4）	Yan et al.,2020
	果实Fruit	X-ChIP	转录因子Transcription factor	SlGRAS4	Liu et al.,2020
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K27me3	Li et al.,2020
	花序原基 Inflorescence primordium	X-ChIP	转录因子 Transcription factor	SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)、 SISTER OF TM3 (STM3)	王晓甜,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Liu et al.,2022
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Ding et al.,2022
莲藕Nelumbo nucifera	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	NnCenH3	朱之轩,2015
莴苣 Lactuca sativa var. ramosa	叶片Leaf	X-ChIP	转录因子Transcription factor	LsSAW1	安光辉,2022
茄子Solanum melongena	根系Root	X-ChIP	转录因子Transcription factor	SmTCP7a	Xiao et al.,2022
甜菜Beta vulgaris	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K9me2	Kowar et al.,2016
白菜Brassica rapa var. glabra	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K27me3	Poza-Viejo et al.,2022
桂花Osmanthus fragrans	花瓣Petal	X-ChIP	转录因子Transcription factor	COfCCD1、OfCCD4	Han et al.,2022
矮牵牛Pharbitis nil	花冠Corolla	X-ChIP	转录因子Transcription factor	ODORANT 1 (ODO1)	Boersma et al.,2022