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N-4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana

文献类型： 外文期刊

作者： Wang, Shuai 1 ; Xie, Hairong 1 ; Mao, Fei 1 ; Wang, Haiyan 1 ; Wang, Shu 2 ; Chen, Zhenglin 1 ; Zhang, Yuxia 1 ; Xu, Zhihui 1 ; Xing, Jinming 1 ; Cui, Zhaokang 3 ; Gao, Xiquan 1 ; Jin, Hongmei 4 ; Hua, Jian 5 ; Xiong, Bo 3 ; Wu, Yufeng 1 ;

作者机构： 1.Nanjing Agr Univ, Acad Adv Interdisciplinary Studies, Bioinformat Ctr, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing, Peoples R China

2.Jiangbei New Area Biopharmaceut Publ Serv Platfor, Nanjing, Peoples R China

3.Nanjing Agr Univ, Coll Anim Sci & Technol, Nanjing, Peoples R China

4.Jiangsu Acad Agr Sci, Inst Agr Resources & Environm, Nanjing, Peoples R China

5.Cornell Univ, Plant Biol Sect, Sch Integrated Plant Sci, Ithaca, NY 14853 USA

关键词： N-4-acetyldeoxycytosine (4acC); 5mC; Histone modification; Gene expression; Arabidopsis thaliana

期刊名称：GENOME BIOLOGY （ 影响因子：17.906； 五年影响因子：20.367 ）

ISSN： 1474-760X

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCI

摘要： Background Direct analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine (5hmC), and N-6-methyladenosine (m6A)/N-6-methyldeoxyadenosine (6mA), are detected in both RNA and DNA, respectively. The modified base N-4-acetylcytosine (ac4C) is well studied in RNAs, but its presence and epigenetic roles in cellular DNA have not been explored. Results Here, we demonstrate the existence of N-4-acetyldeoxycytosine (4acC) in genomic DNA of Arabidopsis with multiple detection methods. Genome-wide profiling of 4acC modification reveals that 4acC peaks are mostly distributed in euchromatin regions and present in nearly half of the expressed protein-coding genes in Arabidopsis. 4acC is mainly located around transcription start sites and positively correlates with gene expression levels. Imbalance of 5mC does not directly affect 4acC modification. We also characterize the associations of 4acC with 5mC and histone modifications that cooperatively regulate gene expression. Moreover, 4acC is also detected in genomic DNA of rice, maize, mouse, and human by mass spectrometry. Conclusions Our findings reveal 4acC as a hitherto unknown DNA modification in higher eukaryotes. We identify potential interactions of this mark with other epigenetic marks in gene expression regulation.

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