Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes
文献类型: 外文期刊
第一作者: Li, Yu-Li
作者: Li, Yu-Li;Song, Shu-hui;Li, Yu-Li;Chen, Ting-ting;Hu, Song-nian;Wang, Xi-liang;Li, Yu-Li;Wu, Yong-Sheng;Huang, Zhi-yuan;Liu, Shuo;Wang, Yinsheng;Dunwell, Thomas L.;Pfeifer, Gerd P.;Dunwell, Jim M.;Wamaedeesa, Raheema;Ullah, Ihsan;Ullah, Ihsan;Wang, Yinsheng
作者机构:
关键词: 5-hydroxymethylcytosine;5hmC profiles;heterochromatin;rice;transposable element
期刊名称:JOURNAL OF EXPERIMENTAL BOTANY ( 影响因子:6.992; 五年影响因子:7.86 )
ISSN:
年卷期:
页码:
收录情况: SCI
摘要: 5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.
分类号: Q94
- 相关文献
作者其他论文 更多>>
-
BRASSINAZOLE RESISTANT 1 delays photoperiodic flowering by repressing CONSTANS transcription
作者:Xu, Xingwen;Chen, Yangbo;Tian, Hao;Yang, Zijian;Liu, Shuo;Li, Xiaopeng;Song, Chunhui;Ye, Zhangli;Guo, Wei;Kong, Dongdong;Hou, Congcong;Li, Legong;Liu, Liangyu;Xu, Xingwen;Chen, Yangbo;Tian, Hao;Yang, Zijian;Liu, Shuo;Li, Xiaopeng;Song, Chunhui;Ye, Zhangli;Guo, Wei;Kong, Dongdong;Hou, Congcong;Li, Legong;Liu, Liangyu;Jiang, Wenbo
关键词:
-
Prevalence and characterization of Cryptosporidium in sika deer from Northern China
作者:Tang, Yan;Liu, Jing;Tang, Yan;Xue, Nian-Yu;Gao, Yang;Gao, Zhen-Qiu;Cao, Hong-Wei;Zhuang, Hong-Di;Li, Jian-Ming;Bao, Guang-Rong;Liu, Shuo
关键词:Cryptosporidium sp.; Sika deer; Prevalence; Subtype; China
-
Nitrogen Monitoring and Sugar Yield Estimation Analysis of Sugar Beet Based on Multisource and Multi-temporal Remote Sensing Data
作者:Wang, Jingyun;Hu, Xiaohang;Liu, Shuo;Li, Yanli;Dong, Xinjiu
关键词:Sugar beet; Unmanned aerial vehicle; Multisource remote sensing data; Multi-temporal; Predictive modeling
-
Organic fertilizer enhances the secretion of microRNAs from tomato roots to facilitate beneficial rhizosphere microorganism expansion and suppress Ralstonia solanacearum proliferation
作者:Li, Hai-Yang;Zhang, Tao;Li, Yang-Kai;Xing, Si-Cheng;Liu, Shuo;Liao, Xin-Di;Li, Hai-Yang;Zhang, Tao;Li, Yang-Kai;Xing, Si-Cheng;Liao, Xin-Di;Liao, Xin-Di;Liao, Xin-Di
关键词:MicroRNA; Organic fertilizer; Ralstonia solanacearum; Rhizomicrobiome; Tomato
-
Effortless rule: Effects of oversized microplastic management on lettuce growth and the dynamics of antibiotic resistance genes from fertilization to harvest
作者:Xing, Si-Cheng;Chen, Jing-Yuan;Qin, Lin-Jie;Long, Tiao;Niu, Shi-Hua;Liu, Shuo;Deng, Wei-Kang;Liao, Xin-Di;Liao, Xin-Di;Xing, Si-Cheng;Liao, Xin-Di;Xing, Si-Cheng;Liao, Xin-Di;Xing, Si-Cheng;Wu, Rui-Ting
关键词:Oversized microplastics; Plastisphere; Lettuce; Antibiotic resistance gene; Simulated digestion
-
Organic fertilizer mitigated the oxidative stress of tomato induced by nanoplastics through affecting rhizosphere soil microorganisms and bacteriophage functions
作者:Tang, Zi-Xuan;Zhai, Hui-Fang;Lai, Hong-Yu;Li, Hai-Yang;Xing, Si-Cheng;Zhao, Liang-Bin;Liu, Shuo;Liao, Xin-Di;Liao, Xin-Di;Xing, Si-Cheng;Liao, Xin-Di;Xing, Si-Cheng;Liao, Xin-Di;Xing, Si-Cheng
关键词:Polystyrene nanoplastics; Oxidative stress; Organic fertilizer; Rhizosphere; Phytohormone
-
Limosilactobacillus reuteri SXDT-32-derived shikimic acid protects against colonic inflammation in piglets by inhibiting the PI3K-Akt pathway
作者:Chen, Ying;Luo, Chengzeng;Zhan, Zhaohan;Liu, Shuo;Teng, Chunran;Mao, Ruixiao;Zhang, Shunfen;Zhang, Xunbozan;Meng, Qingshi;Zhong, Ruqing;Chen, Liang;Zhang, Hongfu;Liu, Shuo;Mao, Ruixiao
关键词:Intestinal inflammation; L. reuteri SXDT-32; PI3K-Akt pathway; Shikimic acid