Histone demethylases have been extensively characterized in plants, yet how their enzymatic activities are regulated remains largely unknown. Here, we identify that MBD8, a protein harboring a putative methyl-CpG-binding domain (MBD), forms a protein complex with the histone demethylase LDL2 in Arabidopsis thaliana. In this complex, MBD8 functions as a cofactor that is required for efficient LDL2-mediated removal of mono- and di-methylation at histone H3 (H3K4me1 and H3K4me2) across the genome. In the Arabidopsis C24 ecotype, loss-of-function mutations in MBD8 and LDL2 result in indistinguishable late-flowering phenotypes, which are consistent with increased enrichment of H3K4me1 and H3K4me2 at the flowering repressor loci MAF1 and MAF5. Importantly, we demonstrate that the rice (Oryza sativa) MBD8 orthologs MBD708, MBD709, and MBD715 also interact with the LDL2 ortholog Hd18 to form a protein complex, and disruption of these components delays flowering by reprogramming the expression of genes associated with floral transition. Collectively, this study reveals an evolutionarily conserved mechanism in which MBD8 orthologs act as cofactors of LDL2 orthologs to regulate histone demethylation and flowering time in plants.

Histone acetyltransferase (HAT) complexes are pivotal regulators of chromatin dynamics, orchestrating transcriptional programs essential for plant development and stress responses in plants. This review synthesizes recent advances in the classification, subunit composition, and functional mechanisms of plant HAT complexes, emphasizing plant-specific characteristics compared to the conserved architecture of HAT complexes. By integrating genetic, biochemical, and structural studies, we delineate how these complexes modulate histone acetylation and coordinate with other chromatin modifications to regulate gene expression. Further research should focus on deciphering the spatiotemporal regulation of HAT complex composition and histone acetylation, and determining the targeting mechanisms of these complexes.

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

Chromatin remodeling complexes serve as crucial regulators of chromatin structure in eukaryotes, governing the transcription, DNA repair, and genome stability. Compared with chromatin remodelers in yeast and animals, plant chromatin remodelers exhibit both conserved and lineage-specific features, which facilitate unique adaptive responses. Cutting-edge approaches in biochemistry, epigenomics, and proteomics are revealing unprecedented insights into plant chromatin remodeling mechanisms, and genetic studies continue to demonstrate their essential roles in maintaining chromatin state homeostasis during plant growth and stress adaptation. This review synthesizes current understanding of plant chromatin remodeling complexes, with particular focuses on their specialized subunit compositions, mechanistic diversity, and integrative roles in epigenetic regulation. Furthermore, we highlight how these complexes interact with histone modifications, DNA methylation pathways, and transcription factor networks to orchestrate plant development and stress responses.

While the role of transcription factors in flower development is well understood, the impact of chromatin remodeling on this process remains largely unclear. We conducted a comprehensive analysis to investigate the coordination of the SAS, BAS, and MAS-type SWI/SNF chromatin-remodeling complexes with transcription factors to regulate chromatin accessibility and gene transcription during flower development in Arabidopsis thaliana. Our findings indicate that the SAS complex binds to numerous genes related to flower development and is responsible for establishing chromatin accessibility of these genes in inflorescences. In contrast, the BAS and MAS complexes exhibit minimal involvement in regulating the accessibility of these genes. The SAS-bound genomic regions and the SAS-dependent accessible regions in infloresences are enriched with sites occupied by multiple MADS family transcription factors involved in flower development. Furthermore, we found that the SAS-dependent accessibility facilitates the binding of the MADS transcription factor AP1 to a subset of its target loci. This study highlights the dynamic role of the SAS complex in modulating the chromatin accessibility and genomic binding of transcription factors during plant development.

Trimethylation of histone H3K4 (H3K4me3) is widely distributed at numerous actively transcribed protein-coding genes throughout the genome. However, the interplay between H3K4me3 and other chromatin modifications in plants remains poorly understood. In this study, we show that the Arabidopsis thaliana ALFIN-LIKE (AL) proteins contain a C-terminal PHD finger capable of binding to H3K4me3 and a PHD-associated AL (PAL) domain that interacts with components of the Polycomb repressive complex 1, thereby facilitating H2A ubiquitination (H2Aub) at H3K4me3-enriched genes throughout the genome. Furthermore, we demonstrate that loss of function of SDG2, encoding a key histone H3K4 methyltransferase, leads to a reduction in H3K4me3 level, which subsequently causes a genome-wide decrease in H2Aub, revealing a strong association between H3K4me3 and H2Aub. Finally, we discover that the PAL domain of AL proteins interacts with various other chromatin-related proteins or complexes, including those involved in regulating H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. Our genome-wide analysis suggests that the AL proteins play a crucial role in coordinating H3K4me3 with multiple other chromatin modifications across the genome.

The Arabidopsis telomere repeat binding proteins TRB1, TRB2, and TRB3 (TRB1/2/3) are components of the PWWP-EPCR-ARID-TRB (PEAT) complex, which is involved in histone acetylation and H2A deubiquitination. TRB1/2/3 also interact with the Polycomb Repressive Complex 2 (PRC2), which mediates H3 lysine 27 trimethylation. This study demonstrates that TRB1/2/3 can form two closely related complexes: TRB1/2/3-HELIX-TURN-HELIX-PROTEIN (TRHT) and TRB1/2/3-HISTONE-DEMETHYLASE (TRHD). The TRHT and TRHD (TRHT/TRHD) complexes occupy numerous common target genes across the genome and are required for H3K4me3 demethylation mediated by the histone demethylase JMJ14. Within the TRHT/TRHD complexes, the transcriptional repressors TRB1/2/3 and NAC050/052 bind to distinct DNA motifs and cooperate to mediate the association of these complexes with their target genes. Compared to PEAT target genes with high H3K4me3 levels and PRC2 target genes with low H3K4me3 levels, TRHT/TRHD target genes display low-to-medium levels of H3K4me3. At TRHT/TRHD target genes, JMJ14-mediated H3K4me3 demethylation is enhanced when these genes are shared with PRC2 target genes and is suppressed when they are shared with PEAT target genes. These findings reveal how the newly identified TRHT/TRHD complexes cooperate with the PEAT and PRC2 complexes to regulate multiple histone modifications and gene transcription across the genome.

The conserved target of rapamycin (TOR) kinase acts as a master regulator of growth by integrating nutrient and environmental signals in eukaryotes. However, how TOR influences chromatin remains poorly understood. Here we identified a multi-subunit complex in Arabidopsis thaliana, termed the chromatin-associated complex for growth (CACG). Our findings indicate that under nutrient-rich conditions, active TOR kinase enhances CACG mRNA translation, which is facilitated by pyrimidine-rich motifs in their 5′ untranslated regions. CACG components co-occupy stress-responsive genes marked by histone acetylation, repressing their transcription to promote growth. Conversely, under nutrient-deficient conditions, inactive TOR reduces CACG mRNA translation, relieving transcriptional repression of stress-responsive genes and leading to increased stress tolerance but impaired growth. These results indicate that the CACG complex acts as a critical nutrient-responsive transcriptional regulator that is required for coordinating plant growth and stress tolerance in a TOR-dependent manner. The molecular mechanism revealed here could aid in developing high-yield crops capable of thriving in adverse environments. A chromatin-associated complex, which is dynamically regulated by TOR kinase at the translational level, functions to suppress the transcription of stress-responsive genes marked by histone acetylation, thereby coordinating plant growth and stress tolerance.

Sodium silicate (Si) treatment can induce resistance in harvested muskmelon fruits (Cucumis melo cv. Yujinxiang) inoculated with Trichothecium roseum, and reduce lesion diameter and incidence of disease spots in the fruit. Moreover, Si treatment increased the production of reactive oxygen species (ROS) and enhanced the activity of phenylalanine ammonia-lyase (PAL) and peroxidase (POD) in the T. roseum-infected fruit. The results of whole-genome bisulfite sequencing indicated that Si treatment increased DNA methylation in muskmelon fruits, with CG sites exhibiting higher methylation levels and the largest number of differentially methylated regions (DMRs). In addition, several DMR-associated genes (DMGs) related to defense responses and the genes involved in ROS metabolism and mitochondrial function were identified, and the changes attributed to hypermethylation in the promoter regions. Therefore, we hypothesized that the changes of genes expression were mainly related to DNA methylation, particularly those involved in the biosynthesis of secondary metabolites and phenylpropanoid biosynthesis.

Although the Arabidopsis thaliana RPD3-type histone deacetylase HDA19 and its close homolog HDA6 participate in SIN3-type histone deacetylase complexes, they display distinct biological roles, with the reason for these differences being poorly understood. This study identifies three angiosperm-specific HDA19-interacting homologous proteins, termed HDIP1, HDIP2, and HDIP3 (HDIP1/2/3). These proteins interact with HDA19 and other conserved histone deacetylase complex components, leading to the formation of HDA19-containing SIN3-type complexes, while they are not involved in the formation of HDA6-containing complexes. While mutants of conserved SIN3-type complex components show phenotypes divergent from the hda19 mutant, the hdip1/2/3 mutant closely phenocopies the hda19 mutant with respect to development, abscisic acid response, and drought stress tolerance. Genomic and transcriptomic analyses indicate that HDIP1/2/3 and HDA19 co-occupy chromatin and jointly repress gene transcription, especially for stress-related genes. An α-helix motif within HDIP1 has the capacity to bind to nucleosomes and architectural DNA, and is required for its function in Arabidopsis plants. These findings suggest that the angiosperm SIN3-type complexes have evolved to include additional subunits for the precise regulation of histone deacetylation and gene transcription.

Seed germination is a critical developmental stage in the lifecycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana Pre-mRNA PROCESSING FACTOR 21 (PRP21) is crucial for regulating the abscisic acid (ABA) response and seed germination. Our RNA deep sequencing and poly(A) tag sequencing analyses reveal that PRP21 is involved in pre-mRNA splicing, genome-wide gene expression, and mRNA 3' end processing, highlighting its multifunctional role in gene regulation. Furthermore, PRP21 interacts with various splicing factors and small nuclear ribonucleoproteins, confirming its involvement in spliceosome assembly. Additionally, we demonstrate that PRP21 negatively regulates the expression of ABA-responsive genes, such as ABI3, ABI5, EM1, and EM6, thereby modulating ABA response and seed germination. Our findings underscore the importance of PRP21 in coordinating transcriptional and post-transcriptional processes and provide insights into the molecular mechanisms underlying seed germination, potentially guiding crop improvement for stress tolerance.

Seed germination is a critical developmental stage in the lifecycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana Pre-mRNA PROCESSING FACTOR 21 (PRP21) is crucial for regulating the abscisic acid (ABA) response and seed germination. Our RNA deep sequencing and poly(A) tag sequencing analyses reveal that PRP21 is involved in pre-mRNA splicing, genome-wide gene expression, and mRNA 3' end processing, highlighting its multifunctional role in gene regulation. Furthermore, PRP21 interacts with various splicing factors and small nuclear ribonucleoproteins, confirming its involvement in spliceosome assembly. Additionally, we demonstrate that PRP21 negatively regulates the expression of ABA-responsive genes, such as ABA INSENSITIVE 3 (ABI3), ABA INSENSITIVE 5 (ABI5), EARLY METHIONINE-LABELED 1 (EM1), and EM6, thereby modulating ABA response and seed germination. Our findings underscore the importance of PRP21 in coordinating transcriptional and post-transcriptional processes and provide insights into the molecular mechanisms underlying seed germination, potentially guiding crop improvement for stress tolerance.

Although histone acetylation and H3K4 trimethylation (H3K4me3) are well-known histone marks associated with active transcription, how they cooperate to regulate transcription remains largely unclear in plants. Our study revealed that the Bromodomain and Extra-terminal (BET) protein GTE4 binds to acetylated histone and forms a complex with the redundant H3K4me3-binding EMSY-Likeproteins EML1 or EML2 (EML1/2) in Arabidopsis thaliana . The eml1 eml2 ( eml1/2 ) double mutant exhibited a morphological phenotype similar to the gte4 mutant, and most of the gte4 -mediated differentially expressed genes were co-regulated in the eml1/2 mutant. Through chromatin immunoprecipitation followed by deep sequencing (ChIP-seq), we found that GTE4 and EML2 co-occupy protein-coding genes enriched with both histone acetylation and H3K4me3, exhibiting a synergistic effect on the association of the GTE4-EML complex with chromatin. The association of GTE4 with chromatin requires both the Bromodomain and the EML-interacting domain. This study identified a previously uncharacterized complex and uncovered how it cooperatively recognizes histone acetylation and H3K4me3 to facilitate gene transcription at the whole-genome level in Arabidopsis. ### Competing Interest Statement The authors have declared no competing interest.

ATP-dependent chromatin remodelers play a crucial role in modifying chromatin configuration by utilizing the energy of ATP hydrolysis. They are involved in various processes, including transcription, DNA replication, and maintaining genome stability. These remodeling remodelers usually form multi-subunit chromatin remodeling complexes in eukaryotes. In plants, chromatin remodeling complexes have diverse functions in regulating plant development and stress response. Recent studies have conducted extensive research on plant chromatin remodeling complexes. This review focuses on recent advances in the classification and composition of plant chromatin remodeling complexes, the protein–protein interactions within the complexes, their impact on chromatin configuration, and their interactions with chromatin modifications and transcription factors.

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 acetylation and H3K4 trimethylation (H3K4me3) are associated with active transcription. However, how they cooperate to regulate transcription in plants remains largely unclear. Our study revealed that GLOBAL TRANSCRIPTION FACTOR GROUP E 4 (GTE4) binds to acetylated histones and forms a complex with the functionally redundant H3K4me3-binding EMSY-like proteins EML1 or EML2 (EML1/2) in Arabidopsis thaliana. The eml1 eml2 (eml1/2) double mutant exhibits a similar morphological phenotype to gte4, and most of the differentially expressed genes in gte4 were coregulated in eml1/2. Through chromatin immunoprecipitation followed by deep sequencing, we found that GTE4 and EML2 co-occupy protein-coding genes enriched with both histone acetylation and H3K4me3, exerting a synergistic effect on the association of the GTE4-EML complex with chromatin. The association of GTE4 with chromatin requires both its bromodomain and EML-interacting domain. This study identified a complex and uncovered how it concurrently recognizes histone acetylation and H3K4me3 to facilitate gene transcription at the whole-genome level in Arabidopsis.

Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.

Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryza sativa . In Arabidopsis , the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL and EAF6). We find that PAGA and SAGA can independently mediate moderate and high levels of histone acetylation, respectively, thereby promoting transcriptional activation. Moreover, PAGA and SAGA can also repress gene transcription via the antagonistic effect between PAGA and SAGA. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.

Using superlubricants to reduce friction and wear can dramatically reduce energy consumption and economic losses in industrial production. In this paper, we report a natural and environmentally friendly lubricant based on phytic acid solution (PA-0) that can achieve robust macroscale liquid superlubrication between PDMS and glass interfaces, and the superlubrication state can be maintained for at least 13 h. Significantly, its superlubrication can also be extended to other friction pair materials, reflecting its robustness and universality as a superlubricant. The calculation of the lubricating film thickness reveals that the superlubrication realized by the PA-0 solution belongs to the mixed lubrication state that comprises boundary lubrication and hydrodynamic lubrication. These findings may advance the practical application of liquid superlubrication.

WRKY transcription factors in plants are known to be able to mediate either transcriptional activation or repression, but the mechanism regulating their transcriptional activity is largely unclear. We found that group IId WRKY transcription factors interact with OBERON (OBE) proteins, forming redundant WRKY-OBE complexes in Arabidopsis thaliana. The coiled-coil domain of WRKY transcription factors binds to OBE proteins and is responsible for target gene selection and transcriptional repression. The PHD finger of OBE proteins binds to both histones and WRKY transcription factors. WRKY-OBE complexes repress the transcription of numerous stress-responsive genes and are required for maintaining normal plant growth. Several WRKY and OBE mutants show reduced plant size and increased drought tolerance, accompanied by increased expression of stress-responsive genes. Moreover, expression levels of most of these WRKY and OBE genes are reduced in response to drought stress, revealing a previously uncharacterized regulatory mechanism of the drought stress response. These results suggest that WRKY-OBE complexes repress transcription of stress-responsive genes, and thereby balance plant growth and stress tolerance.