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Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana
Duren, Zhana1,2; Wang, Yaling3,4; Wang, Jiguang5; Zhao, Xing-Ming6,7; Lv, Le8; Li, Xiaobo9; Liu, Jingdong8; Zhu, Xin-Guang3,4; Chen, Luonan10,11,12,13; Wang, Yong1,2,11
2019-08-12
Source PublicationNPJ SYSTEMS BIOLOGY AND APPLICATIONS
Volume5Pages:11
AbstractTo study systems-level properties of the cell, it is necessary to go beyond individual regulators and target genes to study the regulatory network among transcription factors (TFs). However, it is difficult to directly dissect the TFs mediated genome-wide gene regulatory network (GRN) by experiment. Here, we proposed a hierarchical graphical model to estimate TF activity from mRNA expression by building TF complexes with protein cofactors and inferring TF's downstream regulatory network simultaneously. Then we applied our model on flower development and circadian rhythm processes in Arabidopsis thaliana. The computational results show that the sequence specific bHLH family TF HFR1 recruits the chromatin regulator HAC1 to flower development master regulator TF AG and further activates AG's expression by histone acetylation. Both independent data and experimental results supported this discovery. We also found a flower tissue specific H3K27ac ChIP-seq peak at AG gene body and a HFR1 motif in the center of this H3K27ac peak. Furthermore, we verified that HFR1 physically interacts with HAC1 by yeast two-hybrid experiment. This HFR1-HAC1-AG triplet relationship may imply that flower development and circadian rhythm are bridged by epigenetic regulation and enrich the classical ABC model in flower development. In addition, our TF activity network can serve as a general method to elucidate molecular mechanisms on other complex biological regulatory processes.
DOI10.1038/s41540-019-0106-3
Indexed BySCI
Language英语
Funding ProjectStrategic Priority Research Program of the Chinese Academy of Sciences[XDB13000000] ; National Key R&D Program of China[2017YFA0505500] ; National Key R&D Program of China[2018YFC09105] ; Monsanto Company ; National Natural Science Foundation of China (NSFC)[11871463] ; National Natural Science Foundation of China (NSFC)[61671444] ; National Natural Science Foundation of China (NSFC)[61621003] ; National Natural Science Foundation of China (NSFC)[31771476] ; National Natural Science Foundation of China (NSFC)[61772368] ; National Natural Science Foundation of China (NSFC)[61572363] ; Natural Science Foundation of Shanghai[17ZR1445600] ; Shanghai Municipal Science and Technology Major Project[2018SHZDZX01] ; CAS strategic leading project[XDA08020301] ; ZHANGJIANG LAB
WOS Research AreaMathematical & Computational Biology
WOS SubjectMathematical & Computational Biology
WOS IDWOS:000496187800001
PublisherNATURE PUBLISHING GROUP
Citation statistics
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/50649
Collection应用数学研究所
Corresponding AuthorLiu, Jingdong; Zhu, Xin-Guang; Chen, Luonan; Wang, Yong
Affiliation1.Chinese Acad Sci, Acad Math & Syst Sci, MDIS, CEMS,NCMIS, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, State Key Lab Mol Plant Sci, Shanghai 200032, Peoples R China
4.Chinese Acad Sci, Ctr Excellence Mol Plant Sci, Shanghai 200032, Peoples R China
5.Hong Kong Univ Sci & Technol, State Key Lab Mol Neurosci, Ctr Syst Biol & Human Hlth, Div Life Sci,Dept Chem & Biol Engn, Hong Kong, Peoples R China
6.Fudan Univ, Inst Sci & Technol Brain Inspired Intelligence, Shanghai 200433, Peoples R China
7.Minist Educ, Key Lab Computat Neurosci & Brain Inspired Intell, Shanghai, Peoples R China
8.Bayer US Crop Sci, Monsanto Legal Ent, St Louis, MO 63156 USA
9.Carnegie Inst Sci, Dept Plant Biol, 260 Panama St, Stanford, CA 94305 USA
10.Chinese Acad Sci, Ctr Excellence Mol Cell Sci, Inst Biochem & Cell Biol, Key Lab Syst Biol, Shanghai 200031, Peoples R China
11.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
12.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China
13.Res Ctr Brain Sci & Brain Inspired Intelligence, Shanghai 201210, Peoples R China
Recommended Citation
GB/T 7714
Duren, Zhana,Wang, Yaling,Wang, Jiguang,et al. Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana[J]. NPJ SYSTEMS BIOLOGY AND APPLICATIONS,2019,5:11.
APA Duren, Zhana.,Wang, Yaling.,Wang, Jiguang.,Zhao, Xing-Ming.,Lv, Le.,...&Wang, Yong.(2019).Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana.NPJ SYSTEMS BIOLOGY AND APPLICATIONS,5,11.
MLA Duren, Zhana,et al."Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana".NPJ SYSTEMS BIOLOGY AND APPLICATIONS 5(2019):11.
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