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Histone H3K4 methyltransferase ATX1 positively regulates secondary wall biosynthesis in interfascicular fibers in Arabidopsis

ABSTRACT: Histone H3K4 methyltransferase ATX1 positively regulates secondary wall biosynthesis in interfascicular fibers in Arabidopsis

PROVIDER: PRJNA643778 | ENA |

REPOSITORIES: ENA

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			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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Histone H3K4 methyltransferase ATX1 positively regulates secondary wall biosynthesis in interfascicular fibers in Arabidopsis

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

AtC3H14, a direct target of MYB46, suppress cell elongation and involved in the secondary wall formation.

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

Musashi-type translational regulator controls the buildup of secondary cell wall in Arabidopsis

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.

2023-09-28 | PXD040020 | Pride

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.

2024-09-23 | GSE277439 | GEO

A model system to study secondary growth and bast fibre development: the hemp hypocotyl peeks behind the wall

Project description:Cannabis sativa L. is an annual herbaceous crop grown for the production of long extraxylary fibers, the bast fibers, rich in cellulose and used both in the textile and biocomposite sectors. Despite being herbaceous, hemp undergoes secondary growth and this is well exemplified by the hypocotyl. The hypocotyl was already shown to be a suitable model to study secondary growth in other herbaceous species, namely Arabidopsis thaliana and it shows an important practical advantage, i.e. elongation and radial thickening are temporally separated. This study focuses on the mechanisms marking the transition from primary to secondary growth in the hemp hypocotyl by analysing the suite of events accompanying vascular tissue and bast fiber development. RNA-Seq transcriptomics, imaging and quantification of phytohormones were carried out on four representative developmental stages (i.e. 6-9-15-20 days after sowing) to provide a first comprehensive profiling of the events associated with primary and secondary growth in hemp. This multidisciplinary approach provides cell wall-related snapshots of the growing hemp hypocotyl and identifies marker genes associated with the young (expansins, β-galactosidases and transcription factors involved in light-related processes) and the older hypocotyl (secondary cell wall biosynthetic genes and transcription factors).

2016-11-18 | GSE85144 | GEO

Cell type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis

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

Transcriptome analysis of secondary cell wall development in Medicago truncatula

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

Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase

Project description:Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase

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Expression data from wild-type single muscle fibers

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Ectopic expression of MYB46 identifies transcriptional regulatory genes in secondary wall biosynthesis in Arabidopsis

Project description:MYB46 functions as a transcriptional switch that turns on the genes necessary for secondary wall biosynthesis. Elucidating the transcriptional regulatory network immediately downstream of MYB46 is crucial to our understanding of the molecular and biochemical processes involved in the biosynthesis and deposition of secondary walls in plants. The transcription factors identified here may include direct activators of secondary wall biosynthesis genes. The current study discovered novel hierarchical relationships among the transcription factors involved in the transcriptional regulation of secondary wall biosynthesis and generated several testable hypotheses.

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