Yin‐Na Su

National Institute of Biological Sciences, Beijing

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Xin‐Jian He

National Institute of Biological Sciences, Beijing

She Chen

National Institute of Biological Sciences, Beijing

Lin Li

National Institute of Biological Sciences, Beijing

Xue‐Wei Cai

National Institute of Biological Sciences, Beijing

Dan‐Yang Yuan

National Institute of Biological Sciences, Beijing

Jing Guo

Jilin Agricultural University

Shanshan Chen

Chongqing University

Zhaochen Zhang

National Institute of Biological Sciences, Beijing

Chan‐Juan Wu

Beijing Normal University

Nan Zhao

Tianjin Medical University

Cooperative Institutions

National Institute of Biological Sciences, Beijing

Chinese Academy of Sciences

University of Chinese Academy of Sciences

State Key Laboratory of Plant Genomics

Institute of Genetics and Developmental Biology

Beijing Normal University

Nanjing Agricultural University

Chinese Academy of Medical Sciences & Peking Union Medical College

Shanghai Jiao Tong University

Peking Union Medical College Hospital

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Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation

Journal of Integrative Plant Biology (2022)

Ji‐Yun Shang Xue‐Wei Cai Yin‐Na Su Zhaochen Zhang Xin Wang

Although the Trithorax histone methyltransferases ATX1-5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1-5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylation mainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.

Histone Methylation

DNA demethylation

RNA-Directed DNA Methylation

Epigenomics

H3K4me3

Cancer Epigenetics

10.1111/jipb.13406

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Citations (7)

Arabidopsis histone acetyltransferase complex coordinates cytoplasmic histone acetylation and nuclear chromatin accessibility

Science Advances (2024)

Chan‐Juan Wu Xin Xu Dan‐Yang Yuan Zhenzhen Liu Lianmei Tan

Conserved type B histone acetyltransferases are recognized for their role in acetylating newly synthesized histones in the cytoplasm of eukaryotes. However, their involvement in regulating chromatin within the nucleus remains unclear. Our study shows that the Arabidopsis thaliana type B histone acetyltransferase HAG2 interacts with the histone chaperones MSI2, MSI3, and NASP, as well as the histones H3 and H4, forming a complex in both the cytoplasm and the nucleus. Within this complex, HAG2 and MSI2/3 constitute a histone acetylation module essential for acetylating histone H4 in the cytoplasm. Furthermore, this module works together with NASP to regulate histone acetylation, chromatin accessibility, and gene transcription in the nucleus. This complex enhances chromatin accessibility near transcription start sites while reducing accessibility near transcription termination sites. Our findings reveal a distinct role for the Arabidopsis type B histone acetyltransferase in the nucleus, shedding light on the coordination between cytoplasmic histone acetylation and nuclear chromatin regulation in plants.

Histone acetyltransferase

SAP30

Histone code

10.1126/sciadv.adp1840

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COMPASS functions as a module of the INO80 chromatin remodeling complex to mediate histone H3K4 methylation in Arabidopsis

The Plant Cell (2021)

Ji‐Yun Shang Yujia Lu Xue‐Wei Cai Yin‐Na Su Chao Feng

In the INO80 chromatin remodeling complex, all of the accessory subunits are assembled on the following three domains of INO80: N-terminal domain (NTD), HSA domain, and ATPase domain. Although the ATPase and HSA domains and their interacting accessory subunits are known to be responsible for chromatin remodeling, it is largely unknown how the accessory subunits that interact with the INO80 NTD regulate chromatin status. Here, we identify both conserved and nonconserved accessory subunits that interact with the three domains in the INO80 complex in Arabidopsis thaliana. While the accessory subunits that interact with all the three INO80 domains can mediate transcriptional repression, the INO80 NTD and the accessory subunits interact with it can contribute to transcriptional activation even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. A subclass of the COMPASS histone H3K4 methyltransferase complexes interact with the INO80 NTD in the INO80 complex and function together with the other accessory subunits that interact with the INO80 NTD, thereby facilitating H3K4 trimethylation and transcriptional activation. This study suggests that the opposite effects of the INO80 complex on transcription are required for the balance between vegetative growth and flowering under diverse environmental conditions.

10.1093/plcell/koab187

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The Arabidopsis NuA4 histone acetyltransferase complex is required for chlorophyll biosynthesis and photosynthesis

Journal of Integrative Plant Biology (2022)

Jin‐Xing Zhou Xiao‐Min Su Si‐Yao Zheng Chan‐Juan Wu Yin‐Na Su

Although two Enhancer of Polycomb-like proteins, EPL1A and EPL1B (EPL1A/B), are known to be conserved and characteristic subunits of the NuA4-type histone acetyltransferase complex in Arabidopsis thaliana, the biological function of EPL1A/B and the mechanism by which EPL1A/B function in the complex remain unknown. Here, we report that EPL1A/B are required for the histone acetyltransferase activity of the NuA4 complex on the nucleosomal histone H4 in vitro and for the enrichment of histone H4K5 acetylation at thousands of protein-coding genes in vivo. Our results suggest that EPL1A/B are required for linking the NuA4 catalytic subunits HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY 1（HAM1) and HAM2 with accessory subunits in the NuA4 complex. EPL1A/B function redundantly in regulating plant development especially in chlorophyll biosynthesis and de-etiolation. The EPL1A/B-dependent transcription and H4K5Ac are enriched at genes involved in chlorophyll biosynthesis and photosynthesis. We also find that EAF6, another characteristic subunit of the NuA4 complex, contributes to de-etiolation. These results suggest that the Arabidopsis NuA4 complex components function as a whole to mediate histone acetylation and transcriptional activation specifically at light-responsive genes and are critical for photomorphogenesis.

Histone acetyltransferase

Photomorphogenesis

Histone H4

10.1111/jipb.13227

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Citations (22)

Publisher Correction: Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis

Scientific Reports (2020)

Zhang‐Wei Liu Nan Zhao Yin‐Na Su Shanshan Chen Xin‐Jian He

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

10.1038/s41598-020-79079-3

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Research on the Development of Microteaching and the Applications on Contemporary College English Teaching

Yin‐Na Su Ya‐Hui Hu

In this paper, we conduct research on development of microteaching and the applications on the contemporary college English teaching.Along with the rapid development of higher vocational education, the ministry of education put forward to improve the quality of higher vocational education teaching, it brought opportunities to the development of higher vocational English, also poses a challenge.Based on traditional higher vocational English teaching experience, from student-centered teaching methods, make full use of modern computer technology to multimedia teaching, reasonable practical teaching, training teachers, reform of the examination system and this paper expounds the understanding of higher vocational English teaching reform, and related suggestions are put forward.Through combining the microteaching approach, we optimize the traditional teaching paradigm and the performance which is meaningful and necessary.

Microteaching

10.2991/icsste-16.2016.169

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A histone H3K27me3 reader cooperates with a family of PHD finger‐containing proteins to regulate flowering time in Arabidopsis

Journal of Integrative Plant Biology (2021)

Qian Feng Qiu‐Yuan Zhao Tie‐Nan Zhang Yulu Li Yin‐Na Su

Abstract Trimethylated histone H3 lysine 27 (H3K27me3) is a repressive histone marker that regulates a variety of developmental processes, including those that determine flowering time. However, relatively little is known about the mechanism of how H3K27me3 is recognized to regulate transcription. Here, we identified BAH domain‐containing transcriptional regulator 1 (BDT1) as an H3K27me3 reader. BDT1 is responsible for preventing flowering by suppressing the expression of flowering genes. Mutation of the H3K27me3 recognition sites in the BAH domain disrupted the binding of BDT1 to H3K27me3, leading to de‐repression of H3K27me3‐enriched flowering genes and an early‐flowering phenotype. We also found that BDT1 interacts with a family of PHD finger‐containing proteins, which we named PHD1–6, and with CPL2, a Pol II carboxyl terminal domain (CTD) phosphatase responsible for transcriptional repression. Pull‐down assays showed that the PHD finger‐containing proteins can enhance the binding of BDT1 to the H3K27me3 peptide. Mutations in all of the PHD genes caused increased expression of flowering genes and an early‐flowering phenotype. This study suggests that the binding of BDT1 to the H3K27me3 peptide, which is enhanced by PHD proteins, is critical for preventing early flowering.

PHD finger

10.1111/jipb.13067

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Citations (25)

Three functionally redundant plant-specific paralogs are core subunits of the SAGA histone acetyltransferase complex in Arabidopsis

Molecular Plant (2021)

Chan‐Juan Wu Zhenzhen Liu Wei Long Jin‐Xing Zhou Xue‐Wei Cai

Acetyltransferases

Histone acetyltransferase

10.1016/j.molp.2021.03.014

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Citations (31)

Characterization of an autonomous pathway complex that promotes flowering in Arabidopsis

Nucleic Acids Research (2022)

Peilin Qi Haoran Zhou Qiangqiang Zhao Chao Feng Yong‐Qiang Ning

Abstract Although previous studies have identified several autonomous pathway components that are required for the promotion of flowering, little is known about how these components cooperate. Here, we identified an autonomous pathway complex (AuPC) containing both known components (FLD, LD and SDG26) and previously unknown components (EFL2, EFL4 and APRF1). Loss-of-function mutations of all of these components result in increased FLC expression and delayed flowering. The delayed-flowering phenotype is independent of photoperiod and can be overcome by vernalization, confirming that the complex specifically functions in the autonomous pathway. Chromatin immunoprecipitation combined with sequencing indicated that, in the AuPC mutants, the histone modifications (H3Ac, H3K4me3 and H3K36me3) associated with transcriptional activation are increased, and the histone modification (H3K27me3) associated with transcriptional repression is reduced, suggesting that the AuPC suppresses FLC expression at least partially by regulating these histone modifications. Moreover, we found that the AuPC component SDG26 associates with FLC chromatin via a previously uncharacterized DNA-binding domain and regulates FLC expression and flowering time independently of its histone methyltransferase activity. Together, these results provide a framework for understanding the molecular mechanism by which the autonomous pathway regulates flowering time.

Chromatin immunoprecipitation

H3K4me3

10.1093/nar/gkac551

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Citations (15)

FairBase: a comprehensive database of fungal A-to-I RNA editing

Database (2019)

Jinding Liu Dongbo Wang Yin‐Na Su Kun Lang Rongjing Duan

Frequent A-to-I RNA editing has recently been identified in fungi despite the absence of recognizable homologues of metazoan ADARs ("Adenosine Deaminases Acting on RNA"). In particular, there is emerging evidence showing that A-to-I editing is involved in sexual reproduction of filamentous fungi. Here, we report on the creation of FairBase — a fungal A-to-I RNA editing database that provides a platform for deep exploration of fungal RNA editing to relevant academic communities. This database includes a comprehensive collection of A-to-I editing sites in six filamentous fungal species, together with extensive annotations for each editing site. In FairBase, users can conveniently search editing sites and obtain editing levels for each editing site in various RNA-seq samples. In addition, the pathways involving RNA editing are built in FairBase to help users understand the functions of RNA editing. Furthermore, each fungal species has a genome browser (JBrowse) that allows users to explore A-to-I editing in a genomic context. FairBase is the first fungal RNA editing database.

Genome browser

Guide RNA

10.1093/database/baz018

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Citations (8)