PIF7‐mediated epigenetic reprogramming promotes the transcriptional response to shade in Arabidopsis

Article13 March 2023 Source DataTransparent process PIF7-mediated epigenetic reprogramming promotes the transcriptional response to shade in Arabidopsis Chuanwei Yang Chuanwei Yang State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Data curation, Software, Formal analysis, Funding acquisition, ​Investigation, Visualization Search for more papers by this author Tongdan Zhu Tongdan Zhu orcid.org/0000-0001-9545-976X State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Formal analysis, ​Investigation, Visualization Search for more papers by this author Nana Zhou Nana Zhou State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources Search for more papers by this author Sha Huang Sha Huang State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Formal analysis Search for more papers by this author Yue Zeng Yue Zeng State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Formal analysis Search for more papers by this author Wen Jiang Wen Jiang State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources Search for more papers by this author Yu Xie Yu Xie State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources Search for more papers by this author Wen-Hui Shen Wen-Hui Shen orcid.org/0000-0001-7988-6382 Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France Contribution: Funding acquisition, Writing - original draft, Writing - review & editing Search for more papers by this author Lin Li Corresponding Author Lin Li [email protected] orcid.org/0000-0003-4840-5245 State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Funding acquisition, Writing - original draft, Project administration, Writing - review & editing Search for more papers by this author Chuanwei Yang Chuanwei Yang State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Data curation, Software, Formal analysis, Funding acquisition, ​Investigation, Visualization Search for more papers by this author Tongdan Zhu Tongdan Zhu orcid.org/0000-0001-9545-976X State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Formal analysis, ​Investigation, Visualization Search for more papers by this author Nana Zhou Nana Zhou State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources Search for more papers by this author Sha Huang Sha Huang State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Formal analysis Search for more papers by this author Yue Zeng Yue Zeng State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Formal analysis Search for more papers by this author Wen Jiang Wen Jiang State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources Search for more papers by this author Yu Xie Yu Xie State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources Search for more papers by this author Wen-Hui Shen Wen-Hui Shen orcid.org/0000-0001-7988-6382 Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France Contribution: Funding acquisition, Writing - original draft, Writing - review & editing Search for more papers by this author Lin Li Corresponding Author Lin Li [email protected] orcid.org/0000-0003-4840-5245 State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China Contribution: Resources, Funding acquisition, Writing - original draft, Project administration, Writing - review & editing Search for more papers by this author Author Information Chuanwei Yang1, Tongdan Zhu1, Nana Zhou2, Sha Huang1, Yue Zeng1, Wen Jiang2, Yu Xie1, Wen-Hui Shen3 and Lin Li *,1 1State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China 2State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China 3Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France *Corresponding author. Tel: +86 21 31246736; E-mail: [email protected] The EMBO Journal (2023)42:e111472https://doi.org/10.15252/embj.2022111472 Full textView the full text of the articlePDFDownload PDF of article text and main figures. Peer ReviewDownload a summary of the editorial decision process including editorial decision letters, reviewer comments and author responses to feedback. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract For shade-intolerant plants, changes in light quality through competition from neighbors trigger shade avoidance syndrome (SAS): a series of morphological and physiological adaptations that are ultimately detrimental to plant health and crop yield. Phytochrome-interacting factor 7 (PIF7) is a major transcriptional regulator of SAS in Arabidopsis; however, how it regulates gene expression is not fully understood. Here, we show that PIF7 directly interacts with the histone chaperone anti-silencing factor 1 (ASF1). The ASF1-deprived asf1ab mutant showed defective shade-induced hypocotyl elongation. Histone regulator homolog A (HIRA), which mediates deposition of the H3.3 variant into chromatin, is also involved in SAS. RNA/ChIP-sequencing analyses identified the role of ASF1 in the direct regulation of a subset of PIF7 target genes. Furthermore, shade-elicited gene activation is accompanied by H3.3 enrichment, which is mediated by the PIF7-ASF1-HIRA regulatory module. Collectively, our data reveal that PIF7 recruits ASF1-HIRA to increase H3.3 incorporation into chromatin to promote gene transcription, thus enabling plants to effectively respond to environmental shade. Synopsis In Arabidopsis, the transcription factor PIF7 plays a dominant role in ameliorating the impact shade conditions have on fitness. In this study, a PIF7-ASF1-HIRA regulatory module is found to mediate H3.3 incorporation at a subset of shade-responsive loci, leading to shade-induced gene expression and morphological adaptation. PIF7 recruits the ASF1-HIRA complex under shade conditions ASF1 and HIRA positively regulate shade-induced hypocotyl elongation and define changes in gene expression Shade increases ASF1 and H3.3 enrichment in the chromatin of a subset of PIF7 target genes A PIF7-ASF1-HIRA regulatory module is responsible for H3.3 incorporation in the shade Previous ArticleNext Article Read MoreAbout the coverClose modalView large imageVolume 42,Issue 8,17 April 2023This cover highlights the article Evidence for existence of an apoptosis-inducing BH3-only protein, sayonara, in Drosophila by Yuko Ikegawa, Sa Kan Yoo and colleagues. The study discovers the first cell death-inducing BH3-only protein in fruit flies, termed Sayonara. Sayonara, meaning 'Good bye' in Japanese, originally derives from a popular phrase used by samurai, the Japanese premodern warriors. (Cover concept by the authors; scientific illustration by SciStories) Volume 42Issue 817 April 2023In this issue RelatedDetailsLoading ...