Transcriptome profile of HCT 116p53-/- and HCT 116p53-/- RPL3 KO during Actinomycin (Act D) treatment
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA608302 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To analyse gene expression differences between HCT 116p53-/- and HCT 116p53-/- RPL3 KO and/or during Actinomycin treatment (Act D)
2020-04-13 | GSE145807 | GEO
Project description:Methylation is a common post-translational modification that occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional nuclear localization signal and accumulates in nucleoli. Recombinant METTL18 methylated a single protein in nuclear extracts and in isolated ribosomes from METTL18 knock-out (KO) cells. This protein was identified as 60S ribosomal protein L3 (RPL3), and we also performed an RPL3 interactomics screen and identified METTL18 as the most significantly enriched MTase. Protein mass spectrometry and amino acid analyses revealed that His-245 in RPL3 carries a 3-methylhistidine (3MH; also referred to as t-methylhistidine) modification, which was absent in METTL18 KO cells. In addition, both recombinant and endogenous METTL18 were found to be monomethylated at His-154, likely resulting from auto-methylation, and further corroborating METTL18 as a histidine-specific MTase. Finally, METTL18 KO cells displayed altered pre-rRNA processing, decreased polysomes formation and codon-specific changes in mRNA translation, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. In conclusion, we have here established METTL18 as the second human histidine-specific protein MTase, and demonstrated its functional relevance.
2021-02-28 | GSE146364 | GEO
Project description:Exploring the interactome of human RPL3 by MS-based proteomics.
2021-09-08 | PXD016055 | Pride
Project description:Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation tuning. Indeed, genome-wide ribosome profiling revealed suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a “ribosome code” that ensures proteome integrity in cells.
2022-06-15 | GSE200172 | GEO
Project description:In addition to predominant protein methylation on lysine and arginine residues, histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification has been reported. Moreover, the biological mission of the histidine methylation has remained poorly understood. Here, we reported that human METTL18 is a histidine methyltransferase for ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing proper folding of synthesized proteins. Harnessing in vitro methylation assay with methyl-donor analogue and quantitative mass spectrometry, we identified that His245 of RPL3 is methylated at τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed the stoichiometric modification and suggested its role in translation tuning. Indeed, genome-wide ribosome profiling revealed the suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of “ribosome code”, which ensures proteome integrity in cells.
2022-06-15 | GSE179854 | GEO
Project description:Fusion of the EWS gene to FLI1 produces a fusion oncoprotein that drives an aberrant gene expression program responsible for the development of Ewing sarcoma. We used a homogenous proximity assay to screen for compounds that disrupt the binding of EWS-FLI1 to its cognate DNA targets. A number of DNA-binding chemotherapeutic agents were found to non-specifically disrupt protein binding to DNA. In contrast, actinomycin D was found to preferentially disrupt EWS-FLI1 binding by comparison to p53 binding to their respective cognate DNA targets in vitro. In cell-based assays, low concentrations of actinomycin preferentially blocked EWS-FLI1 binding to chromatin, and disrupted EWS-FLI1-mediated gene expression. Higher concentrations of actinomycin globally repressed transcription. These results demonstrate that actinomycin preferentially disrupts EWS-FLI1 binding to DNA at selected concentrations. Although the window between this preferential effect and global suppression is too narrow to exploit in a therapeutic manner, these results suggest that base-preferences may be exploited to find DNA-binding compounds that preferentially disrupt subclasses of transcription factors.
2013-08-26 | GSE45414 | GEO
Project description:UCRs expression signature of HCT-116 cell lines versus HCT-116 cell line treated with DNA methylation inhibitor 5-aza-2'-deoxycytidine
2010-03-09 | E-MTAB-196 | biostudies-arrayexpress
Project description:Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD (GSE73723). Within these profiles we discovered potentially druggable targets not previously implicated in GVHD, prominently including aurora kinase A (AURKA). In this study, we performed a planned comparison of AURKA gene expression in HCT-recipients with clinical GVHD and compared it to expression in HCT-recipients without clinical GVHD.
2015-11-29 | GSE73809 | GEO
Project description:Cryptosporidium parvum is one of the most important opportunistic enteric parasites, causing severe diarrhea in immunocomprised human and animals. However, few effective control agents were available for this parasite. circular RNA (circRNA) was discovered to play key roles in many diseases, and the well-known regulatory mechanism for circRNAs is that act as miRNA sponges competitively binding to miRNAs to block miRNA-mRNA interaction. Here, using microarray assay, we investigated the expression profiles of circRNAs in HCT-8 cells after the infection of C. parvum IId subtype, the prevalent subtype of China. A total of 178 circRNAs were dysregulated expressed in HCT-8 cells at 24 h post infection (pi) of C. parvum IId subtype.
2022-12-15 | GSE162990 | GEO
Project description:HCT 116 Human Cell Line anticancer drug resistance proteomics
2018-12-27 | MSV000083286 | MassIVE