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| Status |
Public on Aug 02, 2024 |
| Title |
Protein Thermal Stability Changes Induced by the Global Methylation Inhibitor 3-deazaneplanocin A (DZNep) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
To investigate the impact of DZNep on transcription, global protein, and thermal stability changes, we treated HEK293T cells with either vehicle or 100 uM oF DZNep for 48 hrs.
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| Contributor(s) |
Berryhill CA, Doud EH, Hanquier JN, Smith-Kinnaman WR, McCourry DL, Mosley AL, Cornett EM |
| Citation(s) |
39062531 |
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| Submission date |
May 29, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
Evan Cornett |
| E-mail(s) |
evcorn@iu.edu
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| Organization name |
Indiana University
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| Street address |
635 Barnhill Drive
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| City |
Indianapolis |
| State/province |
Indiana |
| ZIP/Postal code |
46202 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA1117934 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE268629_normalized_counts.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE268629_raw_counts.csv.gz |
637.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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