GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5ʹ and 3ʹ ends of its target genes
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ABSTRACT:
PROVIDER: PRJNA565696 | ENA |
REPOSITORIES: ENA
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Project description:The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes; however, its binding did not systematically correlate with gene activation and the mechanism by which GCN5 controls transcription thus remained unclear. To gain insight into GCN5 function, we fine-mapped its genome-wide binding sites and explored the effect of GCN5 loss-of-function on the expression of its target genes, finding that GCN5 has a dual role in the regulation of H3K14ac levels in their 5ʹ and 3ʹ ends. We found that the gcn5 mutation leads to a genome-wide reduction of H3K14ac in the 5ʹ end of some of the GCN5 targets, a phenomenon associated to their down-regulated in the gcn5 mutant. By contrast, an increase of H3K14ac in the 3ʹ end was observed in GCN5 targets that are up-regulated in the gcn5 mutant, indicating that this protein plays a dual role in the control of H3K14ac levels and in the regulation of transcription. Furthermore, changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac in a genome-wide fashion at both 5ʹ and 3ʹ ends, providing evidence for a molecular link between the deposition of these two histone modifications. Finally, we show that GCN5 participates in responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs.
2020-04-28 | GSE137474 | GEO
Project description:Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation. The related data for this are GSE13790 and GSE5227 Data showed expression pattern of gcn5- vs gcn5-clr3- and clr3- vs wild type under KCl stress in S. pombe. Two biological replicates are used with dye-swap labeling.
2010-06-24 | E-GEOD-13817 | biostudies-arrayexpress
Project description: Not available
| S-EPMC7293002 | biostudies-literature
Project description:Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation. The related data for this are GSE13790 and GSE5227
2009-08-01 | GSE13817 | GEO
Project description:Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation. The data in this series showed Gcn5 occupancy and H3K14 acetylation levels in wild type, gcn5- and gcn5-/clr3- cells under KCl stress condition. Related expression data are GSE5227 and GSE13817 Keywords: Chip-chip
2009-08-01 | GSE13790 | GEO
Project description:Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here, we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryzae sativa. In Arabidopsis, the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL, and EAF6). Chromatin immunoprecipitation and sequencing indicate that PAGA and SAGA have both shared and specific target genes, and independently mediate moderate and high levels of histone acetylation, thereby promoting moderately and highly transcriptional activation, respectively. By combining RNA-seq and ChIP-seq data, we found that PAGA and SAGA antagonistically regulate histone acetylation and gene transcription. Genetically, PAGA mutations can partially rescue the developmental defects of the SAGA-specific mutant ada2b-c. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription, and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.
2023-01-09 | GSE217476 | GEO
Project description:rs05-09_histone-acetylase - gcn5 - Different genes show an opposed expression profile in gcn5 compared to hd1. For these genes, the double mutant might show an expression similar to the wild type. - gcn5, hd1 or double mutant gcn5hd1 were grown on MS during 10 days (1.03 boyes stage). Keywords: gene knock out 3 dye-swaps - CATMA arrays
2009-04-10 | E-GEOD-15560 | biostudies-arrayexpress
Project description:rs05-09_histone-acetylase - gcn5 - Different genes show an opposed expression profile in gcn5 compared to hd1. For these genes, the double mutant might show an expression similar to the wild type. - gcn5, hd1 or double mutant gcn5hd1 were grown on MS during 10 days (1.03 boyes stage). Keywords: gene knock out
2009-04-11 | GSE15560 | GEO
Project description:Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating functions of H3K14ac and H3K4me1, we here show that the dual histone modification mark H3K4me1-H3K14ac is recognized by ZMYND8 (also called RACK7) and functions to counteract gene expression. We identified ZMYND8 as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 antagonizes the expression of metastasis-linked genes, and its knockdown increases the cellular invasiveness in vitro and in vivo. The plant homeodomain (PHD) and Bromodomain cassette in ZMYND8 mediates the combinatorial recognition of H3K4me1-H3K14ac and H3K4me0-H3K14ac by ZMYND8. These findings uncover an unexpected role for the signature H3K4me1-H3K14ac in attenuating gene expression and reveal a previously unknown metastasis-suppressive epigenetic mechanism in which ZMYND8's PHD-Bromo cassette couples H3K4me1-H3K14ac with repression of metastasis-linked genes. i) ChIP-Seq data of ZMYND8, JARID1D, H3K4me1, H3K14ac, H3K4me3, and H3K27me3 in normal DU145 cells. ii) ChIP-Seq data of H3K4me1 and H3K4me3 in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells. iii) RNA-Seq data in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells.
2016-07-28 | E-GEOD-82260 | biostudies-arrayexpress
Project description:The role of 3ʹ-5ʹ exonuclease, PARN, in the 3ʹ end miRNA transcriptome in human cells
2019-02-27 | GSE121466 | GEO