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Comparative characterization of the seven H3K4 methyltransferases in Arabidopsis thaliana

ABSTRACT: Comparative characterization of the seven H3K4 methyltransferases in Arabidopsis thaliana

PROVIDER: PRJNA1162426 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30709733.fastq.gz	Fastqsanger.gz
	SRR30709734.fastq.gz	Fastqsanger.gz
	SRR30709735.fastq.gz	Fastqsanger.gz
	SRR30709736.fastq.gz	Fastqsanger.gz
	SRR30709737.fastq.gz	Fastqsanger.gz

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Comparative characterization of the seven H3K4 methyltransferases in Arabidopsis thaliana

Project description:Methylation of H3 lysine 4 (H3K4me) marks transcribed elements of eukaryotic genome, and their distribution alters dynamically through developmental stages and environmental change. These dynamic regulations are likely achieved by combinatorial work of H3K4me writers, which multi-cellular organisms carry multiple copies of. To better understand the chromatin targeting mechanisms of H3K4 methyltransferase in plants, here we comparatively characterized the seven H3K4 methyltransferases in model plants Arabidopsis. This work clarified, in combination with previous results, ATX1-5 (TRX/TRR-type methyltransferase) localizes on loci with specific sets of chromatin modifications and DNA motifs. Notably, ATX3 localizes to binding motifs of ASR3 and RAP2.11 transcriptional factors and also directly interacts with those TFs. ATXR7(SET1-type) and ATXR3 (non-canonical H3K4 methyltransferase) seemed co-transcriptional. Interestingly, ATXR3, the major H3K4me3 methyltransferase in Arabidopsis, was not associated with COMPASS, which suggests H3K4me3 regulation in plants and animals is divergent. Our work provides a foundation for understanding the regulation of H3K4 methyltransferases in plants.

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MLL methyltransferases regulate H3K4 methylation to ensure CENP-A assembly at human centromeres

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ATX3, ATX4, and ATX5 encode putative H3K4 methyltransferases and are critical for plant development

Project description:Methylation of lysine residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily-conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related (ATXR) proteins. Here we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5. We found that they exhibit similar domain structures and expression patterns, and are redundantly required for vegetative and reproductive development. Concurrent disruption of the ATX3, ATX4, and ATX5 genes caused marked reduction in H3K4me2 and H3K4me3 levels genome-wide, and resulted in thousands of genes expressed ectopically. Furthermore, atx3/atx4/atx5 triple mutants resulted in exaggerated phenotypes when combined with the atx2 mutant but not with atx1. Together, we conclude that ATX3, ATX4, and ATX5 are redundantly required for H3K4 di- and trimethylation at thousands of sites located across the genome, and genomic features associated with targeted regions are different from the ATXR3/SDG2-controlled sites in Arabidopsis.

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Histone methyltransferases SDG25/ATX1 regulate heat stress memory by antagonizing DNA remethylation

Project description:Heat stress is a great threat to plant growth because of their sessile lifestyle. Here, we show that histone methyltransferases SDG25 and ATX1 regulate gene expression and antagonize DNA remethylation under recovery stage after long-term high temperature treatment by catalyzing the methylation of histone H3K4 loci.

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Division of labor among H3K4 Methyltransferases Define Distinct Facets of Homeostatic Plasticity

Project description:Histone H3 lysine 4 methylaton (H3K4me), a hallmark of transcriptionally engaged chromatin, is installed by the lysine methyltransferases 2 (KMT2) family of six enzymes in mammals. The six enzymes appear to have arisen from gene duplication of the ancient three enzymes found in the fruit fly. Heterozygous mutations in any of the six enzymes result in monogenic neurodevelopmental disorders, indicating nonredundant yet poorly understood roles of KMT2 family enzymes in neurodevelopment. Recent evidence suggests that histone methyltransferase activity may not be central to KMT2 functions; however, the enzymatic activity is evolutionary conserved, implicating the presence of selective pressure to maintain the catalytic activity. Here, we show that H3K4 methylation is dynamically regulated during prolonged alteration of neuronal activity. The perturbation of H3K4me by the H3.3K4M mutant blocks synaptic scaling, a form of homeostatic plasticity that buffers the impact of prolonged reductions or increases in network activity. Unexpectedly, we found that the six individual enzymes are all necessary for synaptic scaling and that the roles of KMT2 enzymes segregate into evolutionary-defined subfamilies; KMT2A and KMT2B (fly-Trx homologs) for synaptic downscaling, KMT2C and KMT2D (Trr homologs) for upscaling, and KMT2F and KMT2G (dSet homologs) for both directions. Selective blocking of KMT2A enzymatic activity by a small molecule and targeted disruption of the enzymatic domain both blocked the synaptic downscaling and interfered with the activity-dependent transcriptional program. Furthermore, our study revealed specific phases of synaptic downscaling, i.e., induction and maintenance, in which KMT2A and KMT2B play distinct roles. These results suggest that mammalian brains have co-opted intricate H3K4me installation to achieve stability of the expanding neuronal circuits.

2024-08-01 | GSE239471 | GEO

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Project description:The KMT2 (MLL) family of proteins, including the major histone H3K4 methyltransferase found in mammals, exists as large complexes with common subunit proteins and exhibits enzymatic activity. SMYD, another H3K4 methyltransferase, and SET7/9 proteins catalyze the methylation of several non-histone targets, in addition to histone H3K4 residues. Despite these structural and functional commonalities, H3K4 methyltransferase proteins have specificity for their target genes and play a role in the development of various cancers as well as in drug resistance. In this review, we examine the overall role of histone H3K4 methyltransferase in the development of various cancers and in the progression of drug resistance. Compounds that inhibit protein-protein interactions between KMT2 family proteins and their common subunits or the activity of SMYD and SET7/9 are continuously being developed for the treatment of acute leukemia, triple-negative breast cancer, and castration-resistant prostate cancer. These H3K4 methyltransferase inhibitors, either alone or in combination with other drugs, are expected to play a role in overcoming drug resistance in leukemia and various solid cancers.

| S-EPMC8301125 | biostudies-literature

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