数字农科院2.0

Reorganization of the 3D chromatin architecture of rice genomes during heat stress

文献类型: 外文期刊

作者: Zhe Liang; Qian Zhang; Changmian Ji;Guihua Hu;Pingxian Zhang;Yifan Wang;Liwen Yang;Xiaofeng Gu

作者机构:

关键词: A/B compartment; ATAC-seq; Chromatin organization; Heat stress; Hi-C; Plant; Rice; TAD

期刊名称: BMC Biol.

ISSN: 1741-7007

年卷期: 2021 年 19 卷 1 期

页码:

收录情况: JCR(2021版)

摘要: Background: The three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological processes and has been reported to be altered in response to environmental stress. However, the functional changes in spatial genome organization during environmental changes in crop plants are poorly understood. Results: Here we perform Hi-C, ATAC-seq, and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in the size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including HS-related genes, consistent with observed higher HS tolerance in this cultivar. Conclusions: Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice. © 2021, The Author(s).

分类号:

  • 相关文献

[1]Malonylome Analysis In Developing Rice (.Oryza Saliva) Seeds Suggesting T hat Protein Lysine Malonylation Is Well-Conserved And Overlaps With Acetylation And Succinylation Substantially. Peng, Xiaojun,Peng, Zhaohua,Mujahid, Hana,Meng, Xiaoxi,Wang, Cailin,Xing, Shihai. 2018

[2]OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice. Li Y., He Y., Liu Z., Qin T., Wang L., Chen Z., Zhang B., Zhang H., Li H., Liu L., Zhang J., Yuan W.. 2022

[3]White Leaf And Panicle 2, E.ncoding A Pep-Associated Protein, I s Required For Chloroplast Biogenesis Under Heat Stress In Rice. Lv, YS, Shao, GN, Qiu, JH, Jiao, GA, Sheng, ZH, Xie, LH, Wu, YW, Tang, SQ, Wei, XJ, Hu, PS. 2017

[4]The Newly Identified Heat-Stress Sensitive A.lbino 1 Gene Affects C hloroplast Development In Rice. Qiu, ZN, Kang, SJ, He, L, Zhao, J, Zhang, S, Hu, J, Zeng, DL, Zhang, GG, Dong, GJ, Gao, ZY, Ren, DY, Chen, G, Guo, LB, Qian, Q, Zhu, L. 2018

[5]The branchless gene Clbl in watermelon encoding a TERMINAL FLOWER 1 protein regulates the number of lateral branches. Dou J., Yang H., Sun D., Yang S., Sun S., Zhao S., Lu X., Zhu H., Liu D., Ma C., Liu W., Yang L.. 2022

[6]Genome-wide identification studies – A primer to explore new genes in plant species. Safder I., Shao G., Sheng Z., Hu P., Tang S.. 2022

[7]A reciprocal inhibitory module for Pi and iron signaling. Guo M., Ruan W., Zhang Y., Zhang Y., Wang X., Guo Z., Wang L., Zhou T., Paz-Ares J., Yi K.. 2022

[8]Fast Construction Of A Reference G.enome: Challenges And Opportunities U sing 'Royal Gala' Apple As A Case Study. Cong, P.,Chagne, D.,Deng, C. H.,Zhang, C.,Bus, V.,Yao, J. -L.,Sullivan, S.,Tian, Y.,Liachko, I.,Gardiner, S. E.,Gleave, A.. 2018

[9]Genome-Wide Analysis Of The Distinct T.ypes Of Chromatin Interactions I n Arabidopsis Thaliana. Wang, Jingjing,Wang, Jingjing,Meng, Xianwen,Zhou, Yincong,Xue, Jitong,Xue, Jitong,Li, Xue,Chen, Ming,Chen, Ming,Chen, Hongjun,Li, Xue,Fan, Miao,Fan, Miao. 2017

[10]Genome and gene evolution of seahorse species revealed by the chromosome-level genome of Hippocampus abdominalis. He, Libin,Long, Xin,Qi, Jianfei,Wang, Zongji,Huang, Zhen,Wu, Shuiqing,Zhang, Xingtan,Luo, Huiyu,Chen, Xinxin,Lin, Jinbo,Yang, Qiuhua,Huang, Shiyu,Zhou, Qi,Zheng, Leyun. 2021

[11]Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression. Jizeng Jia,Yilin Xie,Jingfei Cheng,Chuizheng Kong,Meiyue Wang,Lifeng Gao,Fei Zhao,Jingyu Guo,Kai Wang,Guangwei Li,Dangqun Cui,Tiezhu Hu,Guangyao Zhao,Daowen Wang,Zhengang Ru,Yijing Zhang. 2021

[12]Identification of a Goat Intersexuality-Associated Novel Variant Through Genome-Wide Resequencing and Hi-C. Guang-Xin E,Dong-Ke Zhou,Zhu-Qing Zheng,Bai-Gao Yang,Xiang-Long Li,Lan-Hui Li,Rong-Yan Zhou,Wen-Hui Nai,Xun-Ping Jiang,Jia-Hua Zhang,Qiong-Hua Hong,Yue-Hui Ma,Ming-Xing Chu,Hui-Jiang Gao,Yong-Ju Zhao,Xing-Hai Duan,Yong-Meng He,Ri-Su Na,Yan-Guo Han,Yan Zeng,Yu Jiang,Yong-Fu Huang. 2021

[13]A Chromosome-Scale Genome Assembly Of C.ucumber (Cucumis Sativus L.). Li, Q, Li, HB, Huang, W, Xu, YC, Zhou, Q, Wang, SH, Ruan, J, Huang, SW, Zhang, Z. 2019

[14]De Novo Assembly Of A W.ild Pear (Pyrus Betuleafolia) G enome. Dong, XG, Wang, Z, Tian, LM, Zhang, Y, Qi, D, Huo, HL, Xu, JY, Li, Z, Liao, R, Shi, M, Wahocho, SA, Liu, C, Zhang, SM, Tian, ZX, Cao, YF. 2019

[15]Chromosome Level Comparative Analysis Of B.rassica Genomes. Wang, WL, Guan, R, Liu, X, Zhang, HR, Song, B, Xu, QW, Fan, GY, Chen, WB, Wu, XM, Liu, X, Wang, JB. 2019

[16]Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Lin, Senjie,Lin, Senjie,Li, Ling,Lin, Xin,Li, Tangcheng,Yu, Liying,Song, Bo,Li, Tangcheng,Lin, Senjie,Song, Yue,Yu, Liying,Lin, Xin,Li, Tangcheng,Li, Ling,Lin, Senjie. 2020

[17]Interactions Between Nanoparticles And Plants: P.hytotoxicity And Defense Mechanisms. Yang, J, Cao, WD, Rui, YK. 2017

[18]Extended Biotic Ligand Model For P.redicting Combined Cu-Zn Toxicity T o Wheat (Triticum Aestivum L.): Incorporating The Effects Of Concentration Ratio, Major Cations And Ph. Wang, XD, Ji, DX, Chen, XL, Ma, YB, Yang, JX, Ma, JX, Li, XX. 2017

[19]Determination Of Perfluoroalkyl Acid Isomers I.n Biosolids, Biosolids-Amended Soils A nd Plants Using Ultra-High Performance Liquid Chromatography Tandem Mass Spectrometry. Zhang, HN, Wen, B, Wen, W, Ma, YB, Hu, XY, Wu, YL, Luo, L, Zhang, SZ. 2018

[20]Transient Expression–Mediated Gene Silencing in Plants and Suppression of Gene Silencing with Viral Suppressors. Li F., Wang A.. 2022

作者其他论文 更多>>