Histone H3K4 methyltransferase ATX1 positively regulates secondary wall biosynthesis in interfascicular fibers in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA643778 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12135871.fastq.gz | Fastqsanger.gz | |||
| SRR12135872.fastq.gz | Fastqsanger.gz | |||
| SRR12135873.fastq.gz | Fastqsanger.gz | |||
| SRR12135874.fastq.gz | Fastqsanger.gz | |||
| SRR12135875_1.fastq.gz | Fastqsanger.gz |
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Project description:Secondary wall thickening in the sclerenchyma cells is strictly controlled by a complex network of transcription factors in vascular plant. However, little is known about the epigenetic mechanism regulating secondary cell wall biosynthesis. Genome-wide analysis revealed that the up-regulation of genes involved in secondary wall formation during stem development is largely coordinated by increasing level of H3K4 tri-methylation. In this study, we identified that ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1), a H3K4-histone methyltransferase, positively regulates secondary wall deposition mainly through activating the expression of secondary wall NAC master switch genes, SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) and NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1).
2020-11-29 | GSE153705 | GEO
Project description:Recently, AtC3H14, a CCCH-type zinc finger protein, was identified as one of the direct targets of MYB46, which is known as a master regulator of secondary wall biosynthesis. AtC3H14 and their homologs (i.e., AtC3H15 and PtrC3H14-1 from Arabidopsis and poplar, respectively) are predominantly expressed in the secondary wall forming tissues. Transgenic Arabidopsis plants overexpressing AtC3H14 (i.e., 35S::AtC3H14 plants) produced dwarfing phenotypes. 35S::AtC3H14 plants developed phloem fibers earlier than wild-type and this phenotype was more pronounced in the roots. Interestingly, ectopic secondary wall thickenings were found in both stems and roots. These phenotypic consequences are successively reproduced from the 35S::AtC3H15 and 35S::PtrC3H14-1 plants. Whole transcriptome GeneChip analysis identified that the ‘cell wall’ and ‘extracellular’-related genes are extremely over-represented in the stem tissues of 35S::AtC3H14 plants. These results suggest that AtC3H14 may act as a negative regulator of cell elongation with modification of cell wall reassembly and be involved in the secondary wall formation in Arabidopsis.
2014-12-05 | GSE23801 | GEO
Project description:Deciphering the mechanism of secondary cell wall/SCW formation in vascular plants is key to understanding their development and the molecular basis of biomass recalcitrance. Although a sophisticated network of transcription factors has been implicated in SCW synthesis in plants, little is known about the implication of RNA-binding proteins in this process. Here we report that two RNA-binding proteins homologous to the animal translational regulator Musashi, Musashi-Like2/MSIL2 and Musashi-Like4/MSIL4, function redundantly to control SCW formation in interfascicular fibers and the setting of biomass recalcitrance. We show that the disruption of MSIL2/4 (msil2-4 mutant) decreases the abundance of lignin in fibers and triggers an hypermethylation of glucuronoxylan that is linked to an over-accumulation of GlucuronoXylan Methyltransferase1/3 (GXM1/3) proteins.
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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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Project description:Spatiotemporal control over developmental programs is vital to all organisms. Here we show that deficiency in cytokinin signaling or biosynthesis leads to early secondary cell wall (SCW) formation in Arabidopsis inflorescence stem that associates with precocious upregulation of a SCW transcriptional cascade controlled by NAC TFs (NSTs/VNDs). We demonstrate that cytokinin signaling through the AHK2/3 and the ARR1/10/12 suppresses the expression of several NSTs/VNDs and SCW formation in the apical portions of stems. Exogenous cytokinin application led to fast downregulation of NST1 and NST3 (NST1/3) and VND6/7 in the WT and reconstituted both proper development and apical-basal gradient of NST1/3 expression in a cytokinin biosynthesis-deficient mutant. We show that AHK2 and AHK3 required functional NST1 or NST3 to control SCW initiation in the interfascicular fibers, further evidencing that cytokinins act upstream of NSTs transcription factors. The premature onset of a rigid SCW biosynthesis and altered expression of NST1/3 and VND6/7 due to cytokinin deficiency led to the formation of smaller tracheary elements (TEs) and impaired hydraulic conductivity. We conclude that cytokinins downregulate NSTs to inhibit premature SCW formation in the apical part of the inflorescence stem, facilitating thus the development of fully functional TEs and interfascicular fibers.
2025-06-24 | GSE300572 | GEO
Project description:Methylation of H3 lysine 4 (H3K4me) marks transcribed elements of the eukaryotic genome, and their distribution alters dynamically through developmental stages and environmental change. These dynamic regulations are likely achieved by the 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 (ATX(R)s) in model plants Arabidopsis. This MS dataset, complemented with the ChIP-seq and AlphaScreen, provides a characterization of ATX(R)s protein. 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, 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.
2025-09-12 | PXD055790 | JPOST Repository
Project description:Deciphering the mechanism of secondary cell wall/SCW formation in vascular plants is key to understanding their development and the molecular basis of biomass recalcitrance. A sophisticated network of transcription factors has been implicated in SCW synthesis in plants, but little is known about the implication of RNA-binding proteins in this process. Here we report that two RNA-binding proteins homologous to the animal translational regulator Musashi, Musashi-Like2/MSIL2 and Musashi-Like4/MSIL4, function redundantly to control SCW formation in interfascicular fibers and the setting of biomass recalcitrance. We show that the disruption of MSIL2/4 decreases the abundance of lignin in fibers and triggers an hypermethylation of glucuronoxylan that is linked to an over-accumulation of GlucuronoXylan Methyltransferase1/3 (GXM1/3) proteins. We demonstrate that MSIL4 binds to the GXM1/3 mRNAs, likely repressing their translation in wild-type plants. Our results reveal cell-type-specific mechanisms underlying SCW formation in Arabidopsis and point to a novel aspect of SCW regulation linking translational repression to regulation of glucuronoxylan methylation.
2023-09-28 | PXD040207 | Pride
Project description:Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase
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Project description:Global transcriptional profiling has been successfully used to identify genes and regulatory pathways in secondary cell wall thickening. A systematic microarray assay of secondary cell wall development along stem maturation in Medicago truncatula was conducted to identify genes and pathways that are involved in lignin/cellulose biosynthesis of secondary wall development.
2016-06-28 | E-MTAB-3909 | biostudies-arrayexpress