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- Title
Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana.
- Authors
Duren, Zhana; Wang, Yaling; Wang, Jiguang; Zhao, Xing-Ming; Lv, Le; Li, Xiaobo; Liu, Jingdong; Zhu, Xin-Guang; Chen, Luonan; Wang, Yong
- Abstract
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. Network biology: transcription factor activity network reveals novel pathway Transcription factor and its combinatorial regulations are fundamentally important in coordination among complex regulatory processes. An international team of researchers led by Yong Wang and Luonan Chen at Chinese Academy of Sciences proposed a novel hierarchical graphical model to infer TF activity network from its mRNA expression, protein co-factors, and downstream regulations. The TF mediated genome-wide gene regulatory network reveals HFR1-HAC1-AG pathway regulating circadian rhythm and flower development in Arabidopsis thaliana. This HFR1-HAC1-AG pathway may enrich the classical ABC model in flower development and imply epigenetic regulation via circadian rhythm. The TF activity network can serve as a general method to elucidate molecular mechanisms on other complex biological regulatory processes.
- Subjects
TRANSCRIPTION factors; ARABIDOPSIS thaliana; FLOWER development; CIRCADIAN rhythms; GENE regulatory networks; PLANT RNA; HISTONE acetylation; PLANTS
- Publication
NPJ Systems Biology & Applications, 2019, Vol 5, Issue 1, pN.PAG
- ISSN
2056-7189
- Publication type
Article
- DOI
10.1038/s41540-019-0106-3