Roles of IDM3 and SDJ1/2/3 in Establishment and/or Maintenance of DNA Methylation in Arabidopsis

The splicing factor U2AF65B regulates cytosine methylation through interacting with DEFECTIVE IN MERISTEM SILENCING 3 in Arabidopsis

U2AF65B is one of the splicing factors that are involved in the recognition of the 3' splicing site and it plays an important role in plant development and stress response through its mRNA splicing function. However, it is not clear whether U2AF65B regulates gene expression in a splicing-independent manner. Through mutant screening and map-based cloning, protein-protein interaction, transcriptomic sequencing, whole-genome bisulfite sequencing and chromatin immunoprecipitation analysis, we investigated the function of U2AF65B in gene silencing in Arabidopsis thaliana. We found in the u2af65b mutant that the exogenous transgene 35S::HYG is activated in expression with decreased DNA methylation on the 35S core-promoter compared with that in the wild-type. Loss of U2AF65B function also globally decreased the methylation of CG, CHG and CHH with a profound effect on CHH methylation in transposons and intergenic sequences. Among the hypomethylated non-CG cytosines in u2af65b, nearly half of them are also hypomethylated in the dms3 mutant. Interestingly, U2AF65B interacts with the RNA-directed DNA methylation (RdDM) pathway component DMS3, and loss of U2AF65B function significantly decreased the enrichment of DMS3 on the targets, including the 35S::HYG transgene and endogenous RdDM loci. Our findings suggest that U2AF65B is a crucial player in RdDM-mediated DNA methylation, partially through promoting the RdDM pathway by interacting with and recruiting DMS3 to the target sequences.

Evolutionary trajectories and subfunctionalization of 2 key methyltransferase regulator subfamilies in plants

DNA methylation, a conserved epigenetic mark in both plants and animals, plays a critical role in growth, development, and adaptability. This study explores the origin, evolution, and functional diversification of 2 key methyltransferase regulators, DNAJ-domain-containing protein 1/2/3 (DNAJ1/2/3) and SU(VAR)3-9 HOMOLOG 1/3 (SUVH1/3), in plants. By analyzing genomic data from 21 algae and 86 land plants, we discovered that DNAJ1/2/3 originated within Magnoliopsida, while SUVH1/3 emerged in ferns and evolved through retrotransposition. Both protein families have undergone multiple duplication events and positive selection throughout plant evolution, resulting in their expansion and functional divergence. In dicotyledons, DNAJ1/2/3 diverged into 3 subclades, whereas SUVH1/3 underwent a common duplication event in its ancestral lineage, resulting in 2 subgroups. Structural domain analysis revealed that the evolution of PHD fingers in DNAJ1/2/3 and AT domains in SUVH1/3, under selective pressure, enhanced their interaction capabilities and contributed to the formation of complexes involved in DNA methylation and demethylation regulation. Expression profile analysis across various plant taxa demonstrated tissue-specific expression patterns, with higher expression levels observed in meristematic tissues and active cell regions. These findings elucidate the evolutionary patterns of DNAJ1/2/3 and SUVH1/3 and offer insights into their functional diversification in plants.

INCREASED DNA METHYLATION 3 forms a potential chromatin remodelling complex with HAIRPLUS to regulate DNA methylation and trichome development in tomato

DNA methylation, a dynamic epigenetic mark influencing gene expression, is regulated by DNA demethylases that remove methylated cytosines at genomic regions marked by the INCREASED DNA METHYLATION (IDM) complex. In Arabidopsis, IDM3, a small α-crystalline domain-containing protein, stabilises the IDM complex. To investigate its role in tomato, we generated slidm3 mutants using genome editing. These mutants displayed a 'hairy' phenotype with increased glandular trichomes, resembling the hairplus (hap) mutant. Affinity purification of SlIDM3-GFP associated proteins identified several chromatin remodelling factors, including HAP. Genome-wide DNA methylation analysis revealed sequence context dependent alterations in the slidm3-1 plants, similar to the hap mutant. CHH methylation was predominantly increased, while CG methylation, particularly in intergenic regions, was decreased in both mutants. This imbalanced methylation suggests the presence of a 'methylstat' mechanism attempting to restore methylation levels at abnormally demethylated sites in the mutants. Comparative functional analysis of differentially methylated regions in the slidm3-1 and hap mutants identified potential methylation-regulated genes that could be linked to the hairy phenotype. Our findings indicate that SlIDM3 may form a chromatin remodelling complex with HAP, epigenetically regulating trichome development.

Characterization of DNA methylation reader proteins in Arabidopsis thaliana

In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted-or read-differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, these results highlight specific context preferences for these proteins, and in particular the ability of MBD2 to bind predominantly to gbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodeling processes in plants.

New insights into the regulation of plant metabolism by O-acetylserine: sulfate and beyond

Under conditions of sulfur deprivation, O-acetylserine (OAS) accumulates, which leads to the induction of a common set of six genes, called OAS cluster genes. These genes are induced not only under sulfur deprivation, but also under other conditions where OAS accumulates, such as shift to darkness and stress conditions leading to reactive oxygen species (ROS) or methyl-jasmonate accumulation. Using the OAS cluster genes as a query in ATTED-II, a co-expression network is derived stably spanning several hundred conditions. This allowed us not only to describe the downstream function of the OAS cluster genes but also to score for functions of the members of the co-regulated co-expression network and hence the effects of the OAS signal on the sulfate assimilation pathway and co-regulated pathways. Further, we summarized existing knowledge on the regulation of the OAS cluster and the co-expressed genes. We revealed that the known sulfate deprivation-related transcription factor EIL3/SLIM1 exhibits a prominent role, as most genes are subject to regulation by this transcription factor. The role of other transcription factors in response to OAS awaits further investigation.

DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development

A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this epigenetic mark in genome-wide gene regulation and plant developmental control is incomplete. Here, we knock out all five known DNA methyltransferases in Arabidopsis, generating DNA methylation-free plants. This quintuple mutant exhibits a suite of developmental defects, unequivocally demonstrating that DNA methylation is essential for multiple aspects of plant development. We show that CG methylation and non-CG methylation are required for a plethora of biological processes, including pavement cell shape, endoreduplication, cell death, flowering, trichome morphology, vasculature and meristem development, and root cell fate determination. Moreover, we find that DNA methylation has a strong dose-dependent effect on gene expression and repression of transposable elements. Taken together, our results demonstrate that DNA methylation is dispensable for Arabidopsis survival but essential for the proper regulation of multiple biological processes.

Our understanding of the extent of involvement of DNA methylation in genome-wide gene regulation and plant developmental control is incomplete. Here, the authors knock out all five known DNA methyltransferases and show the developmental and gene expression changes in the DNA methylation-free Arabidopsis plants.

DNA demethylation affects imprinted gene expression in maize endosperm

Background

DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown.

Results

We analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F₁ hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression.

Conclusions

Our results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02641-x.