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BrCHR39, a novel chromatin remodeling ATPase, positively regulates apical dominance in Brassica rapa

ABSTRACT: BrCHR39, a novel chromatin remodeling ATPase, positively regulates apical dominance in Brassica rapa

PROVIDER: PRJNA813157 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18245026_1.fastq.gz	Fastqsanger.gz
	SRR18245026_2.fastq.gz	Fastqsanger.gz
	SRR18245027_1.fastq.gz	Fastqsanger.gz
	SRR18245027_2.fastq.gz	Fastqsanger.gz
	SRR18245028_1.fastq.gz	Fastqsanger.gz

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BrCHR39, a novel chromatin remodeling ATPase, positively regulates apical dominance in Brassica rapa

Project description:Purpose: The transcriptomic profiling was performed to explain the release of apical dominance due to cell division among stem and bud in BrCHR39-silenced lines . Methods: The stems and axillary buds of the wild-type and BrCHR39-silenced brassica rapa grown for 8 weeks were collected, then immediately dipped in liquid nitrogen for RNA extraction using the TRIzol reagent (Invitrogen, Waltham, MA, USA) and pooled for sequencing. All samples were collected in three biological replicates. After DNaseI treatment, poly (A) mRNA was isolated with oligo (dT) magnetic beads and fragmented to short fragments. Then the first and second strand cDNA were synthesized. And library construction was completed after adding base A and sequencing adapters, end repair, and recovery of the target fragments. Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used to detect the insert size of the library. The qualified cDNA libraries were sequenced by synthesis (SBS) technology using Illumina HiSeq 2500 high-throughput Sequencing platform. Results: In this study, auxin-related genes in the stems of transgenic plants showed a trend of decreasing expression from the beginning of biosynthesis to signal transduction. However, genes about auxin and cytokinin in the buds of transgenic plants were up-regulated totally. Thus we speculated that apical dominance is attributable to differential expression of multiple hormones. Conclusions: Our study provides a detailed analysis of biological replication of transgenic and wild-type transcriptome produced by RNA-seq technology. And specific pathways and associated genes were identified. Our results showed that RNA-seq based transcriptome characterization can provide ideas and basis for subsequent studies to analyze the causes of phenotypic variation. In this study, the reason why the silencing of BrCHR39 gene leads to the weakening of apical dominance was that the auxin signaling pathway was inhibited.

2025-03-02 | GSE197974 | GEO

The Chromatin Remodeling Factor <i>BrCHR39</i> Targets DNA Methylation to Positively Regulate Apical Dominance in <i>Brassica rapa</i>.

Project description:The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH proteins in plants. In this study, we identified a novel SHPRH member BrCHR39 and obtained BrCHR39-silenced transgenic Brassica rapa. In contrast to wild-type plants, transgenic Brassica plants exhibited a released apical dominance phenotype with semi-dwarfism and multiple lateral branches. Furthermore, a global alteration of DNA methylation in the main stem and bud appeared after silencing of BrCHR39. Based on the GO (gene ontology) functional annotation and KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis, the plant hormone signal transduction pathway was clearly enriched. In particular, we found a significant increase in the methylation level of auxin-related genes in the stem, whereas auxin- and cytokinin-related genes were hypomethylated in the bud of transgenic plants. In addition, further qRT-PCR (quantitative real-time PCR) analysis revealed that DNA methylation level always had an opposite trend with gene expression level. Considered together, our findings indicated that suppression of BrCHR39 expression triggered the methylation divergence of hormone-related genes and subsequently affected transcription levels to regulate the apical dominance in Brassica rapa.

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Project description:This SuperSeries is composed of the following subset Series: GSE36822: Clonal competition with alternating dominance in multiple myeloma [244kCGH] GSE36823: Clonal competition with alternating dominance in multiple myeloma [44kCGH] GSE36824: Clonal competition with alternating dominance in multiple myeloma [GEP] Refer to individual Series

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Project description:Mutations in genes encoding subunits of the BAF (BRG1/BRM-associated factor) complex cause various neurodevelopmental diseases. However, the underlying pathophysiology remains largely unknown. Here, we analyzed the function of Brg1, a core ATPase of BAF complexes, in the developing cerebral cortex. Loss of Brg1 causes several morphological defects resembling human malformations of cortical development (MCDs), including microcephaly, cortical dysplasia, cobblestone lissencephaly, and periventricular heterotopia. We demonstrated that neural progenitor cell (NPC) renewal, neuronal differentiation, neuronal migration, apoptotic cell death, pial basement membrane, and apical junctional complexes, which are associated with MCD formation, were impaired after Brg1 deletion. Furthermore, transcriptome profiling indicated that a large number of genes were deregulated. The deregulated genes were closely related to MCD formation, and most of these genes were bound by Brg1. Cumulatively, our study indicates an essential role of Brg1 in cortical development and provides a new possible pathogenesis underlying Brg1-based BAF complex-related neurodevelopmental disorders.

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Microdissection: Transdifferentiation of Root Apical Meristem to Shoot Apical Meristem

2012-05-31 | E-GEOD-30259 | biostudies-arrayexpress

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