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Angiosperm-specific subunits of histone deacetylase complexes are required for the functional specificities of the histone deacetylase HDA19 in development and stress responses [RNA-seq]

ABSTRACT: Angiosperm-specific subunits of histone deacetylase complexes are required for the functional specificities of the histone deacetylase HDA19 in development and stress responses [RNA-seq]

PROVIDER: PRJNA1154239 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30476422_1.fastq.gz	Fastqsanger.gz
	SRR30476422_2.fastq.gz	Fastqsanger.gz
	SRR30476423_1.fastq.gz	Fastqsanger.gz
	SRR30476423_2.fastq.gz	Fastqsanger.gz
	SRR30476424_1.fastq.gz	Fastqsanger.gz

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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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Angiosperm-specific subunits of histone deacetylase complexes are required for the functional specificities of the histone deacetylase HDA19 in development and stress responses [RNA-seq]

Project description:While both the histone deacetylase HDA19 and its close homolog HDA6 can form SIN3-type histone deacetylase complexes, they display specialized biological roles, with the mechanisms of their functional specificities largely unclear. In this study, we identified three previously uncharacterized homologs designated as HDA19-interacting proteins 1, 2, and 3 (HDIP1/2/3). These homologs not only interact with HDA19 but also with other components of the SIN3-type histone deacetylase complexes, including SNLs, MSI1, and HDC1, thereby facilitating the assembly of HDA19-containing complexes but not HDA6-containing ones. HDIP1/2/3 orthologs are found in angiosperms but are absent in other plant species. The hdip1/2/3 and hda19 mutants exhibit highly similar phenotypes in terms of development, abscisic acid response, and drought tolerance. Omics data indicate that HDIP1/2/3 and HDA19 co-occupy chromatin and co-repress gene transcription, particularly at those genes associated with stress responses. An a-helix motif in HDIP1 is capable of binding to the nucleosome as well as the four-way junction DNA that mimics the DNA entry and exit sites of the nucleosome, and is essential for the function of HDIP1 in Arabidopsis plants. These findings suggest that the HDA19-containing SIN3-type histone deacetylase complexes have incorporated additional subunits in angiosperms to support the intricate regulation of histone deacetylation and gene transcription during plant development and stress responses.

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Angiosperm-specific subunits of histone deacetylase complexes are required for the functional specificities of the histone deacetylase HDA19 in development and stress responses

Project description:Angiosperm-specific subunits of histone deacetylase complexes are required for the functional specificities of the histone deacetylase HDA19 in development and stress responses

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

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

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Project description:Arabidopsis thaliana HDA19, Histone deacetylase 19 [Source:UniProtKB/Swiss-Prot;Acc:O22446], is differentially expressed in 52 experiment(s);

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Project description:Arabidopsis thaliana HDA19, Histone deacetylase 19 [Source:UniProtKB/Swiss-Prot;Acc:O22446], is expressed in 15 baseline experiment(s);

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Project description:In this Data Report, we provide an immunoprecipitation (IP)-based analysis of the HDA19 interactome in etiolated Arabidopsis seedlings. We believe that the interactome presented here provides a valuable resource for follow-up research on novel interacting partners of this central protein. The material used for this experiment was derived from hypocotyls of 6-day-old etiolated Arabidopsis seedlings. The dataset contains a total of 6 files, 3 independent biological replicates of each Col-0 (control plants) and 35S::HDA19-GFP plants.

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Angiosperm-specific subunits of histone deacetylase complexes are required for the functional specificities of the histone deacetylase HDA19 in development and stress responses

Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicated that HDA6 and HDA19 function together with other components of the histone deacetylase complexes and co-regulate the expression of a number of genes. HDA6 and HDA19 have been thought to repress gene transcription by histone deacetylation. We found that the histone deacetylase complexes can also repress gene expression via certain histone-deacetylation-independent mechanisms. In the mutants of the histone deacetylase complexes, the expression of a number of stress-induced genes was up-regulated. Several mutants of the histone deacetylase complexes showed severe retardation in growth. Considering that the growth retardation is thought to be a trade-off for the increase of stress tolerance, we predict that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under non-stress conditions.

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