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Genome-wide analysis of histone H3 acetylation levels of wild type, hda6, hdc1, and hda19 in short day conditions [ChIP-seq]

ABSTRACT: Genome-wide analysis of histone H3 acetylation levels of wild type, hda6, hdc1, and hda19 in short day conditions [ChIP-seq]

PROVIDER: PRJNA511982 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8374225.fastq.gz	Fastqsanger.gz
	SRR8374226.fastq.gz	Fastqsanger.gz
	SRR8374227.fastq.gz	Fastqsanger.gz
	SRR8374228.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of histone H3 acetylation levels of wild type, hda6, hdc1, and hda19 in short day conditions [ChIP-seq]

Project description:To investigate whether the expression of upregulated genes in hdc1 and hda19 is assoiated with histone acetylation levels increased in the hdc1 and hda19 mutants, We carried out ChIP-seq to examine histone H3 acetylation at the whole-genome level.

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Genome-wide expression analysis of wild type, hda6, hdc1, and hda19 in short day conditions [RNA-seq]

Project description:To investigate how HDC1, HDA6, and HDA19 regulate gene transcription and flowering time in short day conditions, we performed RNA deep sequencing (RNA-seq) to compare the transcriptomes of wild type, hdc1, hda6, and hda19 mutants grown in short day conditions with two biological repeats.

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Genome-wide expression analysis of wild type, hda6, hdc1, and hda19 in long day conditions [RNA-seq]

Project description:To investigate how HDC1, HDA6, and HDA19 regulate gene transcription and flowering time in long day conditions, we performed RNA deep sequencing (RNA-seq) to compare the transcriptomes of wild type, hdc1, hda6, and hda19 mutants grown in long day conditions.

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Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis [ChIP-Seq]

Project description:Although the Arabidopsis thaliana histone deacetylase HDA19 and its close homolog HDA6 form SIN3-type histone deacetylase complexes, they display distinct biological roles, with the reason for these differences being poorly understood. We has identified three angiosperm-specific HDA19-interacting homologous proteins, termed HDIP1, HDIP2, and HDIP3 (HDIP1/2/3). These proteins interact with HDA19 and other conserved histone deacetylase complex components, leading to the formation of HDA19-containing SIN3-type complexes, while they are not involved in the formation of HDA6-containing ones. While mutants of conserved SIN3-type complex components show phenotypes divergent from the hda19 mutant, the hdip1/2/3 mutant closely mirrors the hda19 mutant in development, abscisic acid signaling, and drought stress tolerance. Omics analyses indicate that HDIP1/2/3 and HDA19 co-occupy chromatin and jointly repress gene transcription, especially for stress-related genes. An α-helix motif within HDIP1 has the capacity to bind to nucleosomes and architectural DNA, and is required for its function in Arabidopsis plants. These findings suggest that the angiosperm SIN3-type complexes have evolved to include additional subunits for the precise regulation of histone deacetylation and gene transcription.

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Genome-wide analysis of wild type, hda6, hdc1, and hda19 in short and long day conditions

Project description:Genome-wide analysis of wild type, hda6, hdc1, and hda19 in short and long day conditions

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SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis

Project description:Although the interplay of covalent histone acetylation/deacetylation and ATP-dependent chromatin remodeling is crucial for the regulation of chromatin structure and gene expression in eukaryotes, the underlying molecular mechanism in plants remains largely unclear. Here we show a direct interaction between Arabidopsis SWI3B, an essential subunit of the SWI/SNF chromatin-remodeling complex, and the RPD3/HDA1-type histone deacetylase HDA6 both in vitro and in vivo. Furthermore, SWI3B and HDA6 co-repress the transcription of a subset of transposons. Both SWI3B and HDA6 maintain transposon silencing by decreasing histone H3 acetylation but increasing histone H3 lysine 9 di-methylation, DNA methylation and nucleosome occupancy. Our findings reveal that SWI3B and HDA6 may act in the same corepressor complex to maintain transposon silencing in Arabidopsis.

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Genome-wide expression analysis of wild type, hda6, hdc1, and hda19 in short day conditions [RNA-seq]

Project description:Genome-wide expression analysis of wild type, hda6, hdc1, and hda19 in short day conditions [RNA-seq]

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H3 Acetylation promotes H2A.Z incorporation into chromatin through SWR1 recruitment to stimulate expression.

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