Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana

doi:10.1038/s41540-019-0106-3

	Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana
	Duren, Zhana 1,2; Wang, Yaling 3,4; Wang, Jiguang 5; Zhao, Xing-Ming 6,7; Lv, Le 8; Li, Xiaobo 9; Liu, Jingdong 8; Zhu, Xin-Guang 3,4; Chen, Luonan10,11,12,13 ; Wang, Yong 1,2,11
	2019-08-12
发表期刊	NPJ SYSTEMS BIOLOGY AND APPLICATIONS
EISSN	2056-7189
卷号	5
发表状态	已发表
DOI	10.1038/s41540-019-0106-3
摘要	To 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.
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收录类别	SCI ; SCIE
语种	英语
资助项目	CAS strategic leading project[XDA08020301]
WOS研究方向	Mathematical & Computational Biology
WOS类目	Mathematical & Computational Biology
WOS记录号	WOS:000496187800001
出版者	NATURE PUBLISHING GROUP
WOS关键词	GENE REGULATORY NETWORKS ; TRANSCRIPTION FACTOR ACTIVITY ; CHROMATIN ACCESSIBILITY ; HISTONE ACETYLATION ; EXPRESSION ; GIGANTEA ; INFORMATION ; COMPONENT ; DATABASE ; PROTEIN
原始文献类型	Article
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/102265
专题	生命科学与技术学院_特聘教授组_陈洛南组
通讯作者	Wang, Yaling; Liu, Jingdong; Zhu, Xin-Guang; Chen, Luonan; Wang, Yong
作者单位	1.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
通讯作者单位	生命科学与技术学院
推荐引用方式 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.
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.
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).