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>>
-
Challenges and countermeasures for developing countries in addressing loss and damage caused by climate change
作者:Liu, Shuo;Li, Yu-E;Wang, Bin;Cai, An-Dong;Liu, Shuo;Li, Yu-E;Wang, Bin;Cai, An-Dong;Feng, Chao;Lan, Hua;Zhao, Ruo-Chen
关键词:Loss and damage; Funding mechanism; Pre-disaster warning and preparedness; Convention negotiations; Countermeasures
-
Evaluation of compost quality and the environmental effects of semipermeable membrane composting with poultry manure using sawdust or mushroom residue as the bulking agent*
作者:Liu, Shuo;Zeng, Jing-Li;Cheng, Zeng-Wen;Pang, Yan-Li;Liao, Xin-Di;Xing, Si-Cheng;Liao, Xin-Di;Liao, Xin-Di;Xing, Si-Cheng;Liao, Xin-Di;Xing, Si-Cheng;Xing, Si-Cheng
关键词:Bulking agent; Compost quality; Environmental effect; Semipermeable membrane composting; Core bacteria
-
Comparative metabolomics combined with genome sequencing provides insights into novel wolfberry-specific metabolites and their formation mechanisms
作者:Long, Qiyuan;Zhang, Changjian;Zhu, Hui;Liu, Shuo;Liu, Yanchen;Zhang, Yuanyuan;Jin, Cheng;Long, Qiyuan;Zhang, Changjian;Zhu, Hui;Zhou, Yutong;Liu, Shuo;Liu, Yanchen;Zhang, Yuanyuan;Jin, Cheng;Ma, Xuemin;An, Wei;Zhao, Jianhua;Zhou, Jun
关键词:metabolome; nutrition; riboflavin; phenyllactate; copy number variation
-
OsbZIP18 Is a Positive Regulator of Phenylpropanoid and Flavonoid Biosynthesis under UV-B Radiation in Rice
作者:Liu, Xueqing;Xin, Jiajun;Yuan, Shiqing;Liu, Shuo;Zhang, Yuanyuan;Jin, Cheng;Liu, Xueqing;Xie, Ziyang;Xin, Jiajun;Yuan, Shiqing;Liu, Shuo;Zhang, Yuanyuan;Jin, Cheng;Sun, Yangyang
关键词:UV-B radiation; metabolites; phenylpropanoid and flavonoids biosynthesis; regulator; rice
-
New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS
作者:He, Liqiang;Sui, Yao;Che, Yanru;Liu, Lihua;Liu, Shuo;Wang, Xiaobing;Cao, Guangping
关键词:rice; free lysine content; genome-wide association study; quantitative trait nucleotide; gene; QTN-by-environment interaction; genomic selection/prediction
-
Sodium butyrate reduces ammonia production in the cecum of laying hens by regulating ammonia-producing bacteria
作者:Liu, Shuo;Hu, Jiaxin;Li, Linfei;Xing, Sicheng;Yang, Yiwen;Liao, Xindi;Liao, Xindi;Liao, Xindi;Liao, Xindi
关键词:laying hen; cecum; ammonia (NH 3 ); sodium butyrate; ammonia-producing bacteria
-
A preliminary study on the root-knot nematode resistance of the cherry plum cultivar Mirabolano 29C
作者:Liu, Jia;Li, Hongwen;Chen, Lijuan;Wang, Dong;Zhang, Guowei;Yao, Meiying;Zhu, Jin;Luo, Deyong;Xie, Xiaodou;Xie, Jialian;Li, Huajia;Li, Ke;Liu, Shuo;Zhang, Yuping
关键词:disease resistance; grafting; phenylpropane pathway; rootstocks; transcriptome sequencing