SIZ1-mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA639284 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12008054_1.fastq.gz | Fastqsanger.gz | |||
| SRR12008054_2.fastq.gz | Fastqsanger.gz |
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Project description:The 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Using a methylation-sensitive PCR (CHOP-PCR)-based forward genetic screen for Arabidopsis DNA hypermethylation mutants, we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation. Dysfunction of SIZ1 leads to hyper-methylation at approximately one thousand genomic regions. SIZ1 physically interacts with ROS1 and mediates the SUMOylation of ROS1. The SUMOylation of ROS1 is reduced in siz1 mutant plants. Compared to that in wild type plants, the protein level of ROS1 is significantly decreased, even though there is an increased level of ROS1 transcripts in siz1 mutant plants. Our results suggest that SIZ1 positively regulates active DNA demethylation by promoting the stability of ROS1 protein through SUMOylation.
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Project description:SUMO E3 Ligase SIZ1-mediated SUMOylation of LBD29 positively regulates lateral root formation in Arabidopsis thaliana
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Project description:Roots are very important at different stages of plant growth, and the formation of lateral roots is essential for strengthening the roots and absorbing nutrients from the soil. Therefore, it is of great significance to uncover the molecular mechanism of lateral root development in plants for understanding plant life process and improving plant adaptation to environment. As an important post-translational modification of small protein types, small ubiquitin-like modifier is involved in many biological processes such as transcriptional regulation, cell cycle regulation, and immune response. SUMO E3 ligase plays a key role in the SUMO process and plays an important role in plant growth and development. In Arabidopsis thaliana, SIZ1 encodes a SUMO E3 ligase, which plays an important role in plant life, especially in stress response. We analyzed the expression sites of SIZ1 and found that it was obviously expressed in lateral roots, especially in the nucleus of lateral roots. Previous studies on SIZ1 mainly focused on biological stress and abiotic stress, but the molecular mechanism of SIZ1 regulating lateral roots has not been studied. We propose a mechanism by which hemicylation of LBD29 mediated by SIZ1 regulates the occurrence of lateral roots in Arabidopsis Thaliana, which provides a new idea and direction for subsequent research on lateral root development.
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Project description:SIZ1, a major plant SUMO E3 ligase, has diverse roles in development and immunity. Although loss-of-function studies have positioned SIZ1 as a negative immune regulator, the pleiotropic effects of its broad substrate repertoire may obscure its core function. Here we report that SIZ1 overaccumulation unexpectedly triggers robust pro-immune responses and cell death, dependent on its E3 ligase activity. We demonstrate that SIZ1 functionally converges on the MOS4-Associated Complex (MAC), a key immune signaling module, with both SIZ1 and the immune receptor SNC1 recruited to MAC-dependent nuclear condensates (MDNCs) upon pathogen challenge. These condensates serve as essential platforms for potentiating immune activation and cell death. Within the MDNC, SIZ1 promotes SUMOylation and stabilizes MAC components, thereby sustaining MDNC integrity during immune responses. Our findings reveal a previously unrecognized pro-immune role for SIZ1 and establish a mechanistic link between SUMOylation, MAC stability, and condensate-mediated immune signaling in plants.
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Project description:Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes. Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of genomic loci. However, the features of ROS1 targets are not well understood. In this study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1 targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants. Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of WT, ros1-4, nrpd1 single mutants and ros1-4/nrpd1doubble mutant
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Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
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Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
2026-02-06 | GSE282072 | GEO
Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
2026-02-06 | GSE282073 | GEO
Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
2026-02-06 | GSE282071 | GEO
Project description:SUMOylation is an essential and highly dynamic post-translational modification that regulates developmental processes and stress adaptations in plants to environmental cues. The global SUMOylation is quickly induced by dehydration and hyperosmotic stresses in plants, while the detailed mechanism underlying such SUMOylation dynamics is largely unknown. Herein, we report key components in osmotic stress and abscisic acid signaling, SNF1-related protein kinase 2s (SnRK2s), phosphorylate SUMO E3 ligase SAP and MIZ1-1 (SIZ1) to stabilize SIZ1 protein under stress conditions. The Ser820 residue is a functional SnRK2 phosphosite and non-phosphorylatable SIZ1S820A is unstable in vivo and in vitro. Under osmotic stress, the rapidly activated protein kinases SnRK2.4 and SnRK2.6 can phosphorylate SIZ1, which enhances the stability of SIZ1, and participates in the response to osmotic stress. However, the instability of SIZ1S820A protein was independent of COP1, indicating that there might be a new degradation mechanism for SIZ1. Our studies suggest that SnRK2s induced phosphorylation regulates SIZ1 stability to precisely modulates SUMOylation dynamics upon osmotic stresses. Additionally, such a reciprocal regulation by SnRK2 and COP1 might be a general regulation machinery that controls the stability of dozens of proteins.
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