Similar Datasets
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.
2025-02-28 | GSE275988 | GEO
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.
2025-02-28 | GSE275986 | GEO
Project description:Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis
| PRJNA1154232 | ENA
Project description:Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis
| PRJNA1154239 | ENA
Project description:Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis [ChIP-Seq]
| PRJNA1154230 | ENA
Project description: Not available
| S-EPMC10701890 | biostudies-literature
Project description:The length of root epidermal cells and their patterning into files of hair-bearing and non-hair cells are genetically determined but respond with high plasticity to environmental cues. Limited phyto-availability of the essential mineral nutrient phosphate (Pi) increases the number of root hairs by longitudinal shortening of epidermal cells and by reprogramming the fate of cells in positions normally occupied by non-hair cells. Through analysis of the root morphology and transcriptional profiles from transgenic Arabidopsis lines with altered expression of the histone deacetylase HDA19, we show that in an intricate interplay of Pi availability and intrinsic factors, HDA19 controls the epidermal cell length, probably by altering the positional bias that dictates epidermal patterning. In addition, HDA19 regulates several Pi-responsive genes that encode proteins with important regulatory or metabolic roles in the acclimation to Pi deficiency. In particular, HDA19 affects genes encoding SPX (SYG1/Pho81/XPR) domain-containing proteins and genes involved in membrane lipid remodeling, a key response to Pi starvation that increases the free Pi in plants. Our data add a novel, non-transcriptionally regulated component of the Pi signaling network and emphasize the importance of reversible post-translational histone modification for the integration of external signals into intrinsic developmental and metabolic programs.
| S-EPMC4623716 | biostudies-literature
Project description:The development and coordination of complex tissues in eukaryotes requires precise spatial control of fate-specifying genes. Although investigations of such control have traditionally focused on mechanisms of transcriptional activation, transcriptional repression has emerged as being equally important in the establishment of gene expression territories. In the angiosperm flower, specification of lateral organ fate relies on the spatial regulation of the ABC floral organ identity genes. Our understanding of how the boundaries of these expression domains are controlled is not complete. Here, we report that the A-class organ identity gene APETALA2 (AP2), which is known to repress the C-class gene AGAMOUS, also regulates the expression borders of the B-class genes APETALA3 and PISTILLATA, and the E-class gene SEPALLATA3. We show that AP2 represses its target genes by physically recruiting the co-repressor TOPLESS and the histone deacetylase HDA19. These results demonstrate that AP2 plays a broad role in flower development by controlling the expression domains of numerous floral organ identity genes.
| S-EPMC3478687 | biostudies-literature
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.
2023-09-19 | PXD045454 | Pride
Project description:Expansions of DNA trinucleotide repeats cause at least 17 inherited neurodegenerative diseases, such as Huntington's disease. Expansions can occur at frequencies approaching 100% in affected families and in transgenic mice, suggesting that specific cellular proteins actively promote (favor) expansions. The inference is that expansions arise due to the presence of these promoting proteins, not their absence, and that interfering with these proteins can suppress expansions. The goal of this study was to identify novel factors that promote expansions. We discovered that specific histone deacetylase complexes (HDACs) promote CTG•CAG repeat expansions in budding yeast and human cells. Mutation or inhibition of yeast Rpd3L or Hda1 suppressed up to 90% of expansions. In cultured human astrocytes, expansions were suppressed by 75% upon inhibition or knockdown of HDAC3, whereas siRNA against the histone acetyltransferases CBP/p300 stimulated expansions. Genetic and molecular analysis both indicated that HDACs act at a distance from the triplet repeat to promote expansions. Expansion assays with nuclease mutants indicated that Sae2 is one of the relevant factors regulated by Rpd3L and Hda1. The causal relationship between HDACs and expansions indicates that HDACs can promote mutagenesis at some DNA sequences. This relationship further implies that HDAC3 inhibitors being tested for relief of expansion-associated gene silencing may also suppress somatic expansions that contribute to disease progression.
| S-EPMC3283555 | biostudies-literature