代表性论文
A. Selected Peer-Reviewed Articles
1.Taolan Zhao , Huan Qing , Jing Sun , Chunyan Liu , Xiuli Hou, Xiang Yu, Ian M. Silverman, Yi Zhang, Brian D. Gregory, Chunming Liu, Wenfeng Qian* and Xiaofeng Cao*. Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biology, 20:189 (2019)
2.Rongxin Yang, Pingchuan Li, Hailiang Mei, Dong Wang, Jing Sun, Chao Yang, Lili Hao, Shouyun Cao, Chengcai Chu, Songnian Hu, Xianwei Song* and Xiaofeng Cao*. Fine-Tuning of MiR528 Accumulation Modulates Flowering Time in Rice. Molecular Plant. 12, 1103–1113, August 5, (2019) (Cover story)
3.Qi Qiu , Hailiang Mei , Xian Deng , Kaixuan He , Qingqing Yao, Baixing Wu, Jixiang Zhang, Falong Lu, Jinbiao Ma* & Xiaofeng Cao*. DNA methylation repels REF6 targeting in Arabidopsis. Nature Communications. 10: 2063 (2019)
4.Shuzhi Zheng , Hongmiao Hu , Huimin Ren, Zhenlin Yang, Qi Qiu, Weiwei Qi, Xinye Liu, Xiaomei Chen, Xiekui Cui, Sisi Li, Bing Zhou, Daye Sun*, Xiaofeng Cao*, Jiamu Du*. The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature- and photoperiod-dependent flowering repressor. Nature Communications, Mar 21;10 (1):1303. doi: 10.1038/s41467-019-09310-x. (2019)
5.Junzhong Liu , Lili Feng , Xueting Gu , Xian Deng , Qi Qiu, Qun Li, Yingying Zhang, Muyang Wang, Yiwen Deng, Ertao Wang, Yuke He, Isabel B？urle, Jianming Li, Xiaofeng Cao*, and Zuhua He*. An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis. Cell Research 29: 379–390 (2019)
6.Peng Liu , Shuaibin Zhang , Bing Zhou , Xi Luo, Xiao Feng Zhou, Bin Cai, Yin Hua Jin, De Niu, Jinxing Lin, Xiaofeng Cao* and Jing Bo Jin*. The Histone H3K4 Demethylase JMJ16 Represses Leaf Senescence in Arabidopsis. The Plant Cell. 31: 430–443, (2019).
7.Wei Zeng , Xinhua Dai , Jing Sun , Yifeng Hou, Xuan Ma, Xiaofeng Cao*, Yunde Zhao, Youfa Cheng*. Modulation of Auxin Signaling and Development by Polyadenylation Machinery. Plant Physiology. 179: 686-699 (2019).
8.Runlai Hang, Zhen Wang, Xian Deng, Chunyan Liu, Bin Yan, Chao Yang, Xianwei Song, Beixin Mo, and Xiaofeng Cao*. Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa. Plant Physiology. 177:381-397 (2018).
9.Hongjing Deng, Jitender Cheema, Hang Zhang, Hugh Woolfenden, Matthew Norris, Zhenshan Liu, Qi Liu, Xiaofei Yang, Minglei Yang, Xian Deng, Xiaofeng Cao* and Yiliang Ding*. Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants. Molecular Plant. 11: 607-622 (2018).
10.Zhenlin Yang, Qi Qiu, Wei Chen, Bei Jia, Xiaomei Chen, Hongmiao Hu, Kaixuan He, Xian Deng, Sisi Li, W. Andy Tao, Xiaofeng Cao*, and Jiamu Du*. Structure of Arabidopsis JMJ14-H3K4me3 complex reveal insight into the substrate specificity of KDM5 subfamily histone demethylase. The Plant Cell. 30: 167-177 (2018).
11.Jianguo Wu, Rongxin Yang, Zhirui Yang, Shengze Yao, Shanshan Zhao, Yu Wang, Pingchuan Li, Xianwei Song, Lian Jin, Tong Zhou, Ying Lan, Lianhui Xie, Xueping Zhou, Chengcai Chu, Yijun Qi, Xiaofeng Cao*, and Yi Li*. ROS Accumulation and Antiviral Defence Control by microRNA528 in Rice. Nature Plant. 3: 16203 (2017)
12.Xiangjin Wei, Xianwei Song, Liya Wei, Shaoqing Tang, Jing Sun, Peisong Hu*, and Xiaofeng Cao*. An Epiallele of Rice AK1 Affects Photosynthetic Capacity. Journal of Integrative Plant Biology, 59 (3): 158-163 (2017).
13.Xia Cui, Falong Lu, Qi Qiu, Bing Zhou, Lianfeng Gu, Shuaibin Zhang, Yanyuan Kang, Xiekui Cui, Xuan Ma, Qingqing Yao, Jinbiao Ma, Xiaoyu Zhang, and Xiaofeng Cao*. REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nature Genetics. 48(6):694-699 (2016).
14.Xian Deng, Tiancong Lu, Lulu Wang, Lianfeng Gu, Jing Sun, Xiangfeng Kong, Chunyan Liu*, and Xiaofeng Cao*. Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5. Proc. Natl. Acad. Sci. USA.113(19): 5447–5452 (2016).
15.Chenlong Li, Lianfeng Gu, Lei Gao, Chen Chen, Chuang-Qi Wei, Qi Qiu, Chih-Wei Chien, Suikang Wang, Lihua Jiang, Lian-Feng Ai, Chia-Yang Chen, Songguang Yang, Vi Nguyen, Yanhua Qi, Michael P Snyder, Alma L Burlingame, Susanne E Kohalmi, Shangzhi Huang, Xiaofeng Cao, Zhi-Yong Wang, Keqiang Wu, Xuemei Chen, and Yuhai Cui. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nature Genetics. 48(6):687-93 (2016).
16.Yong Zhang, Lianfeng Gu, Yifeng Hou, Lulu Wang, Xian Deng, Runlai Hang, Dong Chen, Xiansheng Zhang, Yi Zhang, Chunyan Liu*, and Xiaofeng Cao*. Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein， regulates plant flowering by targeted alternative polyadenylation. Cell Research, 25(7):864-76, doi: 10.1038/cr.2015.77 (2015).
17.Shuaibin Zhang, Bing Zhou, Yanyuan Kang, Xia Cui, Ao Liu, Angelique Deleris , Maxim V. C. Greenberg, Xiekui Cui, Qi Qiu, Falong Lu, James A. Wohlschlegel, Steven E. Jacobsen, and Xiaofeng Cao*. C-terminal domains of histone demethylase JMJ14 interact with a pair of NAC transcription factors to mediate specific chromatin association. Cell Discovery 1:15003, doi:10.1038/celldisc.2015.3 (2015).
18.Liya Wei, Lianfeng Gu, Xianwei Song, Xiekui Cui, Zhike Lu, Ming Zhou, Lulu Wang, Fengyi Hu, Jixian Zhai, Blake C. Meyers, and
Xiaofeng Cao*.
Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice.
Proc. Natl. Acad. Sci. USA, 111 (10): 3877-3882 (2014).
19.Runlai Hang, Chunyan Liu, Ayaz Ahmad, Yong Zhang, Falong Lu, and Xiaofeng Cao*. Arabidopsis Protein Arginine Methyltransferase 3 regulates ribosome biogenesis by affecting precursor ribosomal RNA processing. Proc. Natl. Acad. Sci. USA, 111 (45): 16190-16195 (2014).
20.Hai Zhou, Ming Zhou, Yuanzhu Yang, Jing Li, Liya Zhu, Dagang Jiang, Jingfang Dong, Qinjian Liu, Lianfeng Gu, Lingyan Zhou, Mingji Feng, Peng Qin, Xiaochun Hu, Chengli Song, Jinfeng Shi, Xianwei Song, Erdong Ni, Xiaojin Wu, Qiyun Deng, Zhenlan Liu, Mingsheng Chen, Yao-Guang Liu, Xiaofeng Cao*, and Chuxiong Zhuang*. RNase ZS1 processes UbL40 mRNAs and controls thermo-sensitive genic male sterility in rice. Nature Communications, DOI:10.1038/ncomms5884 (2014).
21.Xiekui Cui, Ping Jin, Xia Cui, Lianfeng Gu, Zhike Lu, Yongming Xue, Liya Wei, Jianfei Qi, Xianwei Song, Ming Luo, Gynheung An, and
Xiaofeng Cao*.
Control of transposon activity by a histone H3K4 demethylase in rice.
Proc. Natl. Acad. Sci. USA, 110: 1953-1958 (2013).
22.Lulu Wang, Xianwei Song, Liangfeng Gu, Xin Li, Shouyun Cao, Chengcai Chu, Xia Cui, Xuemei Chen, and
Xiaofeng Cao*.
NOT2 proteins promote polymerase II-dependent transcription and interact with multiple miRNA biogenesis factors in Arabidopsis.
The Plant Cell, 25:2, 715-727 (2013).
23.Liguo Zhang, Zhijun Cheng, Ruizhen Qin, Yang Qiu, Jiu-Lin Wang, Xiekui Cui, Lianfeng Gu, Xin Zhang, Xiuping Guo, Dan Wang, Ling Jiang, Chuan-yin Wu, Haiyang Wang, Xiaofeng Cao, and Jianmin Wan. Identification and Characterization of an Epi-Allele of FIE1 Reveals a Regulatory Linkage between Two Epigenetic Marks in Rice. The Plant Cell, 24: 4407-4421 (2012).
25.Xianwei Song, Dekai Wang, Lijia Ma, Zhiyu Chen, Pingchuan Li, Xia Cui, Chunyan Liu, Shouyun Cao, Chengcai Chu, Yuezhi Tao, and
Xiaofeng Cao*.
Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development.
The Plant Journal, 71:378-389 (2012).
26.Xianwei Song, Pingchuan Li, Jixian Zhai, Ming Zhou, Lijia Ma, Bin Liu, Dong-Hoon Jeong, Mayumi Nakano, Shouyun Cao, Chunyan Liu, Chengcai Chu, Xiu-Jie Wang, Pamela J. Green, Blake C. Meyers, and
Xiaofeng Cao*.
Roles of DCL4 and DCL3b in rice phased small RNA biogenesis.
The Plant Journal, 69:462-474 (2012).
28.Xian Deng, Lianfeng Gu,
Chunyan Liu, Tiancong Lu, Falong Lu, Zhike Lu, Peng Cui, Yanxi Pei, Baichen Wang, Songnian Hu, and
Xiaofeng Cao*.
Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing.
Proc. Natl. Acad. Sci. USA, 107:19114-19119 (2010).
32.Lifang Niu, Yong Zhang, Yanxi Pei, Chunyan Liu, and Xiaofeng Cao*. Redundant requirement for a pair of PROTEIN ARGININE METHYLTRANSFERASE4 homologs for the proper regulation of Arabidopsis flowering time. Plant Physiology 148:490-503 (2008).
33.Falong Lu, Guanglin Li, Xia Cui, Chunyan Liu, Xiu-Jie Wang, and Xiaofeng Cao*. Comparative Analysis of JmjC Domain-containing Proteins Reveals the Potential Histone Demethylases in Arabidopsis and Rice. Journal of Integrative Plant Biology. 50 (7): 886–896 (2008).
34.Jixian Zhai, Jun Liu, Bin Liu, Pingchuan Li, Blake C. Meyers, Xuemei Chen, and Xiaofeng Cao*. Small RNA-directed Epigenetic Natural Variation in Arabidopsis thaliana. PLoS Genetics 4(4): e1000056 (2008).
35.Lifang Niu, Falong Lu, Yanxi Pei, Chunyan Liu, and Xiaofeng Cao*. Regulation of Flowering Time by a Protein Arginine Methyltransferase, AtPRMT10. EMBO Reports 8(12):1190-1195 (2007)
36.Bin Liu, Zhiyu Chen, Xianwei Song, Chunyan Liu, Xia Cui, Xianfeng Zhao, Jun Fang, Wenying Xu, Huiyong Zhang, Xiujie Wang, Chengcai Chu, Xingwang Deng, Yongbiao Xue, and Xiaofeng Cao*. Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. The Plant Cell, 19: 2705-2718 (2007).
37.Dongsheng Yan, Yong Zhang, Lifang Niu, Yi Yuan, and Xiaofeng Cao*. Identification and characterization of two closely related histone H4 arginine 3 methyltransferases in Arabidopsis thaliana. Biochemical Journal, 408: 113-121 (2007).
38.Yanxi Pei, Lifang Niu, Falong Lu, Chunyan Liu, Jixian Zhai, Xiangfeng Kong, and Xiaofeng Cao*. Mutations in the type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis thaliana. Plant Physiology, 144: 1913-1923 (2007).
39.Weiwei Deng, Chunyan Liu, Yanxi Pei, Xian Deng, Lifang Niu, and Xiaofeng Cao*. Involvement of the histone acetyltransferase AtHAC1 in the regulation of flowering time via repression of FLC in Arabidopsis thaliana. Plant Physiology, 143: 1660-1668 (2007).
40.Yong Ding, Xia Wang, Lei Su, Jixian Zhai, Shouyun Cao, Dongfen Zhang, Chunyan Liu, Yuping Bi, Qian Qian, Zhukuan Cheng, Chengcai Chu*, and Xiaofeng Cao*. SDG714, a histone H3K9 methyltransferase involves in Tos17 DNA methylation and transposition in Oryza sativa L. The Plant Cell 19:9-22 (2007).
41.Bin Liu, Pingchuan L , Xin Li, Chunyan Liu, Yunru Cao, Chengcai Chu, Xiaofeng Cao*. Loss of Function of OsDCL1 Affects MicroRNA Accumulation and Causes Developmental Defects in Rice. Plant Physiology 139: 296–305 (2005).
42.Daniel Zilberman, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington and Steven E. Jacobsen. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology, 14: 1214-1220 (2004).
43.Xiaofeng Cao, Werner Aufsatz, Daniel Zilberman, M. Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology, 13: 2212-2217 (2003).
44.Daniel Zilberman, Xiaofeng Cao and Steven E. Jacobsen. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 299: 716-719 (2003).
45.Xiaofeng Cao and Steven E. Jacobsen. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Current Biology, 12: 1138-1144 (2002a).
46.Xiaofeng Cao and Steven E. Jacobsen. Locus specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl. Acad. Sci., USA, 99: 16491-16498 (2002b).
47.James P. Jackson, Anders M. Lindroth, Xiaofeng Cao, and Steven E. Jacobsen. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature, 416:556-560 (2002).
48.Lianna Johnson, Xiaofeng Cao, and Steven E. Jacobsen. Interplay between two epigenetic marks: DNA methylation and histone H3 lysine 9 methylation. Current Biology, 12: 1360-1367 (2002).
49.Anders Lindroth#, Xiaofeng Cao#, James Jackson #, Daniel Zilberman, Claire M. McCallum, Steven Henikoff and Steven E. Jacobsen. Requirement of Chromomethylase3 for maintenance of CpXpG methylation. Science, 292: 2077-2080 (2001). (#These authors contributed equally to this work).
50.Xiaofeng Cao, Nathan M. Springer, Michael G. Muszynski, Ronald L. Phillips, Shawn Kaeppler, and Steven E. Jacobsen. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl. Acad. Sci. USA, 97: 4979-4984 (2000).
51.Xiaofeng Cao, Sally W. Rogers, Juliet Butler, Leonard Beevers, and John C. Rogers. Structural requirements for ligand binding by a probable plant vacuolar sorting receptor. The Plant Cell, 12: 493-506 (2000).
52.Xiaofeng Cao, Paul Linstead, Fred Berger, Joe Kieber, and Liam Dolan. Differential ethylene sensitivity of epidermal cells is involved in the establishment of cell pattern in the Arabidopsis root. Physiologia Plantarum, 106: 311-317 (1999).
B. Selected Invited Articles
53.Xianwei Song , Yan Li , Xiaofeng Cao*, and Yijun Qi*. MicroRNAs and Their Regulatory Roles in Plant--Environment Interactions. Annu. Rev. Plant Biol. 70:489-525 (2019).
54.Xian Deng, Qi Qiu, Kaixuan He and Xiaofeng Cao*. The seekers: how epigenetic modifying enzymes find their hidden genomic targets in Arabidopsis. Current Opinion in Plant Biology. 45:75-81 (2018)
55.Cheng-Guo Duan*, Jian-Kang Zhu*, Xiaofeng Cao*. Retrospective and perspective of plant epigenetics in China. Journal of Genetics and Genomics. 45: 621e638 (2018).
56.Xianwei Song and Xiaofeng Cao*. Context and Complexity: Analyzing Methylation in Trinucleotide Sequences. Trends in Plant Science. 22 (5) 351-353 (2017).
57.Xianwei Song and Xiaofeng Cao*. Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice. Current Opinion in Plant Biology. 36: 111-118 (2017).
58.Xian Deng and Xiaofeng Cao*. Roles of pre-mRNA splicing and polyadenylation in plant development. Current Opinion in Plant Biology. 35: 45-53 (2017).
59.Xian Deng, Xianwei Song, Liya Wei, Chunyan Liu, and Xiaofeng Cao*. Epigenetic Regulation and the Epigenomic Landscape in Rice. National Science Review. 3(3): 309-327 (2016).
60.Liya Wei and Xiaofeng Cao*. The effect of transposable elements on phenotypic variation: insights from plants to humans. SCIENCE CHINA Life Sciences. 59(1): 24-37 (2016).
62.Xiekui Cui and Xiaofeng Cao*. Epigenetic regulation and functional exaptation of transposable elements in higher plants. Current Opinion in Plant Biology. 21: 83-88 (2014).
64.The EPIC Planning Committee: Fred Berger,
Xiaofeng Cao, Vicki Chandler, Liz Dennis, Rob Martienssen, Blake Meyers, Craig Pikaard, Jim Peacock, Eric Richards, Doris Wagner, Detlef Weigel, Vincent Colot, Roger Deal, Caroline Dean, Joe Ecker, Mary Gehring, Zhizhong Gong, Brian Gregory, Gutierrez Rodrigo, Jose Gutierrez-Marcos, Mitsuyasu Hasebe, Il-Doo Hwang, Steven E. Jacobsen, Tetsuji Kakutani, Jiayang Li, Scott Michaels, Yoo-Sun Noh, Nick Provart, and Matt Vaughn.
Reading the Second Code: Mapping epigenomes to understand plant growth, development, and adaptation to the environment. The Plant Cell, 24: 2257-2261 (2012).
