Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protein Thermal Stability Changes Induced by the Global Methylation Inhibitor 3-deazaneplanocin A (DZNep)

ABSTRACT: Protein Thermal Stability Changes Induced by the Global Methylation Inhibitor 3-deazaneplanocin A (DZNep)

PROVIDER: PRJNA1117934 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29225442_1.fastq.gz	Fastqsanger.gz
	SRR29225442_2.fastq.gz	Fastqsanger.gz
	SRR29225443_1.fastq.gz	Fastqsanger.gz
	SRR29225443_2.fastq.gz	Fastqsanger.gz
	SRR29225444_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Protein Thermal Stability Changes Induced by the Global Methylation Inhibitor 3-deazaneplanocin A (DZNep)

Project description:DZNep (3-deazaneplanocin A) is commonly used to reduce lysine methylation. DZNep inhibits S-adenosyl-L-homocysteine hydrolase (AHCY), preventing the conversion of S-adenosyl-L-homocysteine (SAH) into L-homocysteine and reducing the level of S-adenosylmethionine (SAM). As a result, the SAM to SAH ratio decreases, an indicator of the methylation potential within a cell. Many studies have characterized the impact of DZNep on histone lysine methylation or in specific cell or disease contexts. Recently, protein thermal stability has provided a new dimension for studying the mechanism of action of small molecule inhibitors. In addition to ligand binding, post-translational modifications and protein-protein interactions impact thermal stability. Here, we sought to characterize protein thermal stability changes induced by DZNep treatment in HEK293T cells using the Protein Integral Solubility Alteration (PISA) assay. DZNep treatment altered the thermal stability of 135 proteins, with over half previously reported to be methylated at lysine residues. In addition to thermal stability, we identify changes in transcript and protein abundance after DZNep treatment to distinguish between direct and indirect impacts on thermal stability. Nearly one-third of the proteins with altered thermal stability had no changes at the transcript or protein level. Of these thermally altered proteins, CDK6 had a stabilized methylated peptide, while its unmethylated counterpart was unaltered. Multiple methyltransferases were among the proteins with thermal stability alteration, including DNMT1, potentially due to changes in SAM/SAH levels. This study systematically evaluates DZNep’s impact on the transcriptome, the proteome, and the thermal stability of proteins.

2024-08-02 | GSE268629 | GEO

DMSO control and DZNep treated MOLM-14 cells

Project description:We demonstrated that 3-Deazaneplanocin A (DZNep), a histone methyltransferase inhibitor, induce robust apoptosis in AML cells through increased ROS production and ER stress. We identified a core gene signature including TXNIP, a major redox control molecule which is crucial in DZNep-induced apoptosis.

2011-07-01 | GSE30315 | GEO

DMSO control and DZNep treated MOLM-14 cells

2011-07-01 | E-GEOD-30315 | biostudies-arrayexpress

Real-time quantitative PCR analysis of DZNep treated B cell Lymphoma cell line Jeko-1

Project description:Jeko-1 cells were culture with or without PRC2 inhibitor 3-deazaneplanocin A (DZNep)(1uM) for 72hrs. We used TaqMan® Human MicroRNA Array to quantitate miRNA expression profile regulated by PRC2.

2012-08-11 | GSE40019 | GEO

Real-time quantitative PCR analysis of DZNep treated B cell Lymphoma cell line Jeko-1

Project description:Jeko-1 cells were culture with or without PRC2 inhibitor 3-deazaneplanocin A (DZNep)(1uM) for 72hrs. We used TaqManM-BM-. Human MicroRNA Array to quantitate miRNA expression profile regulated by PRC2. qPCR miRNA expression profiling.

2012-08-11 | E-GEOD-40019 | biostudies-arrayexpress

Vitamin C promotes anti-leukemia of DZNep in Acute Myeloid Leukemia

Project description:The epigenetic treatment by 3-Deazaneplanocin A (DZNep), a histone methyltransferase inhibitor, shows great potential against acute myeloid leukemia (AML). However, the variant sensitivity and incomplete response to DZNep are commonly observed. We reveal that vitamin C (Vc) dramatically promotes DZNep response against leukemic cells in different cell lines and primary AML samples. To examine the molecular determinants underlying Vc enhanced anti-leukemia effect of DZNep, we conducted a genome-wide RNA sequencing and a gene ontology (GO) enrichment analysis of differentially expressed mRNAs in each group was performed.

2022-09-30 | GSE192629 | GEO

The S-adenosyl-homosteine hydrolase inhibitor DZNeP unspecifically affects histone methylation patterns in embryos and results in developmental aberrations

Project description:3-deazaneplanocin A (DZNeP) is a promising cancer drug affecting the methylation status of histone lysine residues. To investigate the specificity and mode of action of DZNeP, zebrafish embryos displaying high histone methyltransferase activity were cultured with DZNeP and histone methylation (H3K4me3, H3K9me3, H3K27me3) was mapped by ChIP-chip genome-wide promoter at post-MBT stage (5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff.

2014-11-21 | GSE53209 | GEO

Integrated changes in thermal stability and proteome abundance during altered growth and metabolic cell states.Integrated changes in thermal stability and proteome abundance during altered growth and metabolic cell states.

Project description:Altered thermal solubility measurement techniques are emerging as powerful tools to assess ligand binding, post-translational modification, protein-protein interactions, and many other cellular processes that affect protein state under various cellular conditions. Thermal solubility or stability profiling techniques are enabled on a global proteomic scale by employing the latest generation of isobaric tagging reagents that facilitate multiplexing capacity required to measure the proteome across thermal gradients. Key among these is thermal proteomic profiling (TPP), which requires 8-10 isobaric tags per gradient and multiple sets of proteomic analyses to measure different replicates and conditions. Furthermore, using thermal profiling techniques to measure protein state across different conditions also requires measurements of difference in protein abundance. Here, we use PISA to assess protein abundance and thermal stability.

2024-02-14 | PXD031800 | Pride

The S-adenosyl-homosteine hydrolase inhibitor DZNeP unspecifically affects histone methylation patterns in embryos and results in developmental aberrations

2014-11-21 | E-GEOD-53209 | biostudies-arrayexpress

Proteome-wide analysis of protein thermal stability in Arabidopsis

Project description:In the present project, we applied quantitative mass spectrometry to profile the thermal stability of the Arabidopsis proteome in living cells.

2023-05-06 | PXD033755 |

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data