Nse4-FLAG CHIP-seq analysis in gcn5, ubp8, ada2 deletion background in S.pombe, control wt 501 - no tag
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ABSTRACT:
PROVIDER: PRJEB57799 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10509528_1.fastq.gz | Fastqsanger.gz | |||
| ERR10509528_2.fastq.gz | Fastqsanger.gz | |||
| ERR10509529_1.fastq.gz | Fastqsanger.gz | |||
| ERR10509529_2.fastq.gz | Fastqsanger.gz | |||
| ERR10509530_1.fastq.gz | Fastqsanger.gz |
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Project description:to find functional relevance between SMC5/6 complex and SAGA histone acetyltransferase complex in Schizosaccharomyces pombe by chromatin immunoprecipitation of Nse4-FLAG tagged protein from gcn5, ubp8 and ada2 deletion strains and 2 control strains (WT - Nse4-FLAG, 501 - no tag).
2023-02-20 | E-MTAB-12401 | biostudies-arrayexpress
Project description:The SAGA complex is a highly conserved histone acetyltransferase (HAT) complex in eukaryotes, playing crucial role in regulating gene transcription throughout organismal development. The complex consists of two core components: GCN5, the HAT subunit, and ADA2, which primarily functions as an adaptor, facilitating interactions between GCN5 and other proteins and enhancing the complex’s accessibility to nucleosomes. Beyond its well-established roles, we discovered that, in rice, ADA2 possesses an evolutionary conserved intrinsically disordered region (IDR) that directs the SAGA complex to form nuclear condensates. Moreover, we identified a physical interaction between ADA2 and ATP-citrate lyase subunit A2 (ACLA2), leading to the formation of a GCN5-ADA2-ACLA2 (GAA) complex. Both GCN5 and ACLA2 exhibit phase separation in vivo, a process that is dependent on ADA2. Within these condensates, ACL contributes to the production and enrichment of acetyl-CoA, thereby promoting histone acetylation. Genetic evidence showed that knock-out or suppression of the three indicated genes collectively resulted in diminished meristem zones at both root tips and inflorescences, accompanied by a significant reduction in genomic H3K9 acetylation and transcriptional attenuation of essential genes for meristem function. In summary, our findings unveiled a novel mechanism for HAT in modulating gene transcription and plant development, in which the GAA complex phase separates and enriches acetyl-CoA metabolites within the nuclear puncta to facilitate the acetylation of histones at target genes.
2025-09-23 | GSE300491 | GEO
Project description:The SAGA complex of Saccharomyces cerevisiae contains greater than 20 components that acetylate and deubiquitylate nucleosomal histones. Its acetyltransferase, Gcn5 preferentially acetylates histones H3 and H2B and is regulated through interactions with Ada2 and Ngg1/Ada3. The N-terminal region of Ada2 contains a SANT domain that contacts Gcn5 near its catalytic site. Sequence alignments of Ada2 homologues indicate a conserved ~120 amino acid residue central region that interacts with Ngg1.To examine the function of this central region, we constructed ada2 alleles with mutations of clustered conserved residues. One of these alleles, ada2-RLR, resulted in a ~3-fold reduction in transcriptional activation of the PHO5 gene and growth changes that parallel deletion of ada2. Microarray analyses further revealed that ada2-RLR alters expression of a subset of those genes affected by deletion of ada2. Keywords: yeast, Ada2, SAGA complex, gene expression, genetic modification
2008-11-11 | GSE11377 | GEO
Project description:Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E Transcriptomes. And quantitatively analyze the cell signaling pathways that regulated by the studied mutants. Methods: total mRNA was extracted from U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E.llumina compatible libraries were prepared by using the KAPA Stranded mRNA-Seq Library Preparation Kit for Illumina® platforms (KAPA Biosystems). In brief, 250 ng of total RNA was enriched for poly-A-tailed mRNA by using Kapa’s mRNA Capture beads. Poly-A-enriched RNA was fragmented to a median size of 150 bp by using chemical fragmentation and converted into double-stranded cDNA with dUTP incorporated into the second cDNA strand. The ends of the double-stranded cDNA were polished, 5’-phosphorylated, and 3’-A-tailed for the ligation of indexed adapters. Adapter-ligated DNA fragments were amplified by 8 cycles of PCR. The strand with incorporated dUTP was not amplified. The resulting libraries were quantified by qPCR and assessed for size distribution by using the 4200 TapeStation (Agilent Technologies), and then multiplexed, 4 per pool, and sequenced on the Illumina’s NextSeq500 by using the mid-output, 75-bp paired-end read format. Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the human genome and quantified the expression of protein coding genes in the U251 cells of WT Gcn5 and Gcn5 Y645A mutant/WT DLST and DLST R224A/K226E mutant. Altered expression of 3 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E Transcriptomes. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that Gcn5 Y45A mutant and DLST R224A/K226E mutant, which reduce histone H3 K79 succinylation, can regulate several cell signaling pathways that important for cancer cell proliferation.
2017-12-13 | GSE98050 | GEO
Project description:Histone lysine benzoylation may occur by Gcn5-catalyzed and nonenzymatically ways in vivo. In this project, we identified several Kbz sites on Xenopus laevis octamer in the absence or presence Gcn5-Ada2 complex in vitro, respectively. The number 672 represents the data in the absence of Gcn5-Ada2, and the number 674 represents the data that in the presence of Gcn5-Ada2.
2022-05-19 | PXD030110 | Pride
Project description:Histone post-translational modifications (PTMs) are critical for processes such as transcription. The more notable among these are the non-acetyl histone lysine acylation modifications such as crotonylation, butyrylation and succinylation. However, the biological relevance of these PTMs is not fully understood because their regulation is largely unknown. Here, we set out to investigate whether the main histone acetyltransferases in budding yeast, Gcn5 and Esa1, possess crotonyltransferase activity. In vitro studies revealed that the Gcn5-Ada2-Ada3 (ADA) and Esa1-Yng2-Epl1 (Piccolo NuA4) histone acetyltransferase complexes have the capacity to crotonylate histones. Mass spectrometry analysis revealed that ADA and Piccolo NuA4 crotonylate lysines in the N-terminal tails of histone H3 and H4, respectively. Functionally, we show that crotonylation selectively affects gene transcription in vivo in a manner dependent on Gcn5 and Esa1. Thus, we identify the Gcn5- and Esa1-containing ADA and Piccolo NuA4 complexes as bona fide crotonyltransferases that promote crotonylation-dependent transcription.
2019-11-06 | PXD015488 | Pride
Project description:Firstly, wild type seedlings that had germinated in root tubes for 14 days were taken to prepare protoplasts. The GCN5-FLAG transient expression vector was transformed into wild type protoplasts. The protoplasts were collected and purified by Flag beads. After quality testing of the samples, phosphorylation mass spectrometry sequencing of GCN5 was performed.
2025-10-28 | PXD066361 | Pride
Project description:PArtner and Localizer of BRCA2 (PALB2) is essential to maintain genome stability in human cells. Upon DNA damage by double DNA strand breaks, PALB2 is required to repair DNA by homologous recombination. In undamaged conditions, PALB2 protects coding regions, by preventing DNA stress due to collisions between transcription and replication machineries. PALB2 associates with chromatin, which is essential to fulfill its function in genome stability maintenance, however molecular mechanisms regulating PALB2 chromatin association remain unknown. In our previous published study describing the KAT2A/B(GCN5/PCAF)-acetylome (Fournier et al., Nat.Comm. 2016, doi: 10.1038/ncomms13227) we have identified PALB2 as an acetylated protein target of the acetyltransferases KAT2A (GCN5) and KAT2B (PCAF) in vivo. KAT2A/B-acetylated sites of PALB2 were mapped within its DNA/Chromatin association domain. In this current study, we have conducted in vitro acetyltransferase (AT) assays, by mixing purified recombinant GST-tagged PALB2 full-length (FL) and PALB2 fragment P2.2 which associates with DNA/chromatin (from residues 295-610), with Flag-PCAF, Flag-GCN5 and Flag-GCN5 catalytic mutant (mut), followed by proteomics analysis to map PALB2 acetylated lysines by KAT2A(GCN5) and KAT2B(PCAF) in vitro. PALB2 FL and P2.2 alone, or PALB2 FL and P2.2 mixed with GCN5 catalytic mutant, were used as negative controls.
2023-03-10 | PXD014681 | Pride
Project description:This study aims to understand the impact of adenosine deaminase 2 (ADA2) on human monocyte-derived macrophages
2021-09-24 | GSE184572 | GEO
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