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OsbHLH002-OSH1 module orchetrates the secondary cell wall formation in rice (ChIP-Seq)

ABSTRACT: OsbHLH002-OSH1 module orchetrates the secondary cell wall formation in rice (ChIP-Seq)

PROVIDER: PRJNA978610 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24798248_1.fastq.gz	Fastqsanger.gz
	SRR24798248_2.fastq.gz	Fastqsanger.gz
	SRR24798249_1.fastq.gz	Fastqsanger.gz
	SRR24798249_2.fastq.gz	Fastqsanger.gz

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OsbHLH002-OSH1 module orchetrates the secondary cell wall formation in rice (RNA-Seq)

Project description:OsbHLH002-OSH1 module orchetrates the secondary cell wall formation in rice (RNA-Seq)

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Transcriptomes of Rice internode before and after heading

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AtMAN6 coordinates cell growth and secondary cell wall formation in xylem development

Project description:We observed that the Arabidopsis endo-1,4-mannanase gene AtMAN6 is involved in the formation of cell walls in vascular tissues. In the inflorescence stem, the man6 mutant had smaller vessel cells with thicker secondary cell walls and shorter fiber cells. Elongation growth was reduced in the root, and secondary cell wall deposition in vessel cells occurred early. Overexpression of AtMAN6 resulted in the inverse phenotypes of the man6 mutant. AtMAN6 was discovered on the plasma membrane and was specifically expressed in vessel cells during its early development. The AtMAN6 protein degraded galactoglucomannan to produce oligosaccharides, which caused secondary cell wall deposition in vessel and fiber cells to be delayed. Transcriptome analysis revealed that the expression of genes involved in the secondary cell wall synthesis pathway was changed in both man6 mutant and AtMAN6 overexpression plants. AtMAN6's carboxyl-terminal cysteine repeats motif (CCRM) was found to facilitate homodimerization and is required for its activity. According to the findings, the oligosaccharides produced by AtMAN6 hydrolysis may act as a signal to mediate this coordination between cell expansion and SCW deposition.

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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.

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AtMAN6 coordinates cell growth and secondary cell wall formation in xylem development

Project description:AtMAN6 coordinates cell growth and secondary cell wall formation in xylem development

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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).

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Project description:To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur. Transcriptomes of rice third or the fourth internodes were analyzed at 17, 8, and 1 day before, and 6, 13, and 35 days after heading Please note that the current data were normalized together with additional 143 sample data available in GEO and the list of the sample accessions is provided in Series supplementary file [normalized_together_GSMs.txt].

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OsbHLH002-OSH1 module orchetrates the secondary cell wall formation in rice (ChIP-Seq)

Project description:To explore the in-depth mechanism of how OsbHLH002-OSH1 complex promotes SCW development We performed chromatin immunoprecipitation sequencing (ChIP-seq) to investigate the genome-wide binding sites of OsbHLH002 using Osbhlh002-1 gOsbHLH002-3FLAG.

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