Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA355037 | ENA |
REPOSITORIES: ENA
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Project description:We explore the genome-wide occupancy of 4 different chromatin regulating complexes encoded in S. cerevisiae. We provide the data for histone acetyltransferases Gcn5 and Esa1 and histone deacetylases Hst1 and Rpd3/Sin3 under rich growth condition (YPD medium). We also include the occupancy data for RNA polymerase II under the same growth condition.
2005-11-03 | E-WMIT-2 | biostudies-arrayexpress
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.
2021-06-10 | GSE166089 | GEO
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.
2021-06-10 | GSE166088 | GEO
Project description:Lysine acetylation is one of the most prevalent post-translational modifications and has since been found to regulate histone functions and affect chromatin structure and gene expression. Here, we charactered Rpd3, a histone deacetylase of Beauveria bassiana, played important roles in the deacetylation of histone H3 and H4. We unveil the role of Rpd3 in asexual development and show that a ΔRpd3 mutant strain has severe growth defects and is defective in conidiophores and blastospores development. Proteomic analyses indicated that Rpd3 functions in asexual development and virulence and multiple stress responses via broad genetic pathways in B. bassiana. Therefore, we conclude that BbRpd3 is vital for asexual development, virulence and multiple stress responses in Beauveria bassiana.
2021-08-12 | PXD006713 | Pride
Project description:Lysine acetylation is one of the most prevalent post-translational modifications and has since been found to regulate histone functions and affect chromatin structure and gene expression. Here, we charactered Rpd3, a histone deacetylase of Beauveria bassiana, played important roles in the deacetylation of histone H3 and H4. We unveil the role of Rpd3 in asexual development and show that a ΔRpd3 mutant strain has severe growth defects and is defective in conidiophores and blastospores development. Acetylomic analyses indicated that Rpd3 functions in asexual development and virulence and multiple stress responses via broad genetic pathways in B. bassiana. Therefore, we conclude that BbRpd3 is vital for asexual development, virulence and multiple stress responses in Beauveria bassiana.
2021-08-12 | PXD006714 | Pride
Project description:Histone deacetylase inhibitor enhanced salinity stress response
| PRJNA292335 | ENA
Project description:Previous results suggest that Bmh might inhibit the activity of the transcription factor Adr1 after binding to Adr1-dependent promoters. In a strain lacking the two major histone deacetylases, Hda1 and Rpd3 (hdac?), Adr1 is bound to its target promoters recruiting what appears to be an inactive RNA ploymerase II preinitiation complex (PIC). To determine whether Bmh activity inhibits this inactive PIC and the generality of this effect on glucose-repressed gene expression, the mRNA profiles of wild type, bmh mutant, hdac mutant, and bmh hdac mutant cells grown in high glucose medium were compared. Total RNAs were purified from triplicate cultures of W303-1A (wild type), YLL1087 (bmh1-ts bmh2?), CTY-TY44 (hda1? rpd3?) and KBY3 (bmh1-ts bmh2? hda1? rpd3?) cells exponentially growing in YP broth containing 5% glucose and then profiled using Affymetrix Yeast 2.0 arrays.
2013-01-15 | E-GEOD-40116 | biostudies-arrayexpress
Project description:Class I histone deacetylases (HDAC) critically contribute to Ewing sarcoma pathogenesis II
| PRJNA683020 | ENA
Project description:To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. Global gene expression analysis showed that Rpd3 partially regulated gene expression upon heat shock. The Hsf1 and Msn2/4 transcription factors are the main regulators of gene activation in response to heat stress. RPD3-deficient cells had impaired activation of Msn2/4-dependent genes, while activation of genes controlled by Hsf1 was deacetylase independent. Rpd3 bound to heat stress-dependent promoters through the Msn2/4 transcription factors, allowing entry of RNA Pol II and activation of transcription upon stress. Finally, we found that the large, but not the small Rpd3 complex regulated cell adaptation in response to heat stress.
2010-04-23 | GSE17514 | GEO
Project description:Cmr1 (changed mutation rate 1) is a largely uncharacterized nuclear protein that has recently emerged in several global genetic interaction and protein localization studies. It clusters with proteins involved in DNA damage and replication stress response, suggesting a role in maintaining genome integrity. Under conditions of proteasome inhibition or replication stress, this protein localizes to distinct sub-nuclear foci termed as intranuclear quality control (INQ) compartments, which sequester proteins for their subsequent degradation. Interestingly, it also interacts with histones, chromatin remodelers and modifiers, as well as with proteins involved in transcription including subunits of RNA Pol I and Pol III, but not with those of Pol II. It is not known whether Cmr1 plays a role in regulating transcription of Pol II target genes. Here, we show that Cmr1 is recruited to the coding regions of transcribed genes of S. cerevisiae. Cmr1 occupancy correlates with the Pol II occupancy genome-wide, indicating that it is recruited to coding sequences in a transcription-dependent manner. Cmr1-enriched genes include Gcn4 targets and ribosomal protein genes. Furthermore, our results show that Cmr1 recruitment to coding sequences is stimulated by Pol II CTD kinase, Kin28, and the histone deacetylases, Rpd3 and Hos2. Finally, our genome-wide analyses implicate Cmr1 in regulating Pol II occupancy at transcribed coding sequences. However, it is dispensable for maintaining co-transcriptional histone occupancy and histone modification (acetylation and methylation). Collectively, our results show that Cmr1 facilitates transcription by directly engaging with transcribed coding regions. ChIp-chip experiments were perfomed to determine genome-wide distribution of Cmr1 in WT and gcn4Î cells (S. cerevisiae). Rpb3 occupancy in WT and cmr1Î cells was also determined to reveal the changes in Pol II occupancy in the absence of Cmr1. The WT and mutant strains were grown in Synthetic complete and cells were indcued for Gcn4 by treating with Sulfometuron methyl for 30 minutes and processed for chromatin immunoprecipitation using antibodies against Myc and Rpb3 (subunit of Pol II).
2016-07-01 | E-GEOD-77016 | biostudies-arrayexpress