Protein arginine methylation in Trypanosomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA610785 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11250083_1.fastq.gz | Fastqsanger.gz | |||
| SRR11250083_2.fastq.gz | Fastqsanger.gz | |||
| SRR11250084_1.fastq.gz | Fastqsanger.gz | |||
| SRR11250084_2.fastq.gz | Fastqsanger.gz | |||
| SRR11250085_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Protein arginine methylation in Trypanosomes
| PRJNA610785 | ENA
Project description:We report on mRNA expression changes in Trypanosoma brucei with Zinc finger protein ZFP3 variants R68/71F, R68/71K, and an RNAi knockdown. Abundance of mRNA transcripts was determined with short read RNA-Seq after variant expression or RNAi knockdown induction with doxycycline. Differentially expressed transcripts were identified across all conditions.
2020-03-07 | GSE146506 | GEO
Project description:Protein methylation is involved in different processes including gene expression regulation, epigenetics, and nucleotide metabolism. Identification of methylated proteins is difficult as methyl groups are small, and do not introduce significant changes in protein hydrophobicity or charge state. The most effective analytical method to date is relative enrichment by pan-specific antibodies and methylation specific binding domains. Here, we present a novel and unbiased chemical strategy to enrich and identify sites of lysine and arginine methylations. This approach makes use of the property that methylation does not alter the charge state of lysine and arginine. This approach revealed over 793 methylation events including 211 arginine and 585 lysine methylation sites in HEK 293 Cells. This strategy proves to be convenient, effective and versatile, with the potential of analyzing other PTMs on both lysine and arginine.
2016-08-16 | PXD001689 | Pride
Project description:Alternative polyadenylation (APA) has recently been recognized as a universal mechanism for gene regulation, but it remains unclear how APA is controlled. Here we report that the Arabidopsis thaliana Protein Arginine Methyltransferase 10 (AtPRMT10) regulates global APA with its protein partner HLP1, a conserved hnRNP A/B protein. HLP1 binds preferentially to A-rich and U-rich cis-elements around polyadenylation sites, thereby linking AtPRMT10 to the control of APA through protein-protein interactions. AtPRMT10 mutations cause significant proximal-to-distal poly(A) site shifts largely overlapping with those in hlp1-1 mutants. Proximal polyadenylation is maintained by AtPRMT10-directed methylation and is mediated in part by methylation of HLP1 at specific arginine residues. Our findings demonstrate that arginine methylation of an RNA-binding protein adds a novel layer of regulation to widespread alternative polyadenylation.
2019-01-01 | GSE69904 | GEO
Project description:The covalent attachment of methyl groups to the side-chain of arginine residues is known to play essential roles in regulation of transcription, protein function and RNA metabolism. The specific N-methylation of arginine residues is catalyzed by a small family of gene products known as protein arginine methyltransferases; however, very little is known about which arginine residues become methylated on target substrates. Here we describe an unbiased methodology that combines single-step immunoenrichment of methylated peptides with high-resolution mass spectrometry to identify endogenous arginine mono-methylation (MMA) sites. We thereby identify 1,027 site-specific MMA sites on 494 human proteins, discovering numerous novel mono-methylation targets and confirming the majority of currently known MMA substrates. Nuclear RNA-binding proteins involved in RNA processing, RNA localization, transcription, and chromatin remodeling are prominently found modified with MMA. Despite this, MMA sites prominently are located outside RNA-binding domains as compared to the proteome-wide distribution of arginine residues. Quantification of arginine methylation in cells treated with Actinomycin D uncovers strong site-specific regulation of MMA sites during transcriptional arrest. Interestingly, several MMA sites are down-regulated after a few hours of under transcriptional arrest. In contrast, the corresponding di-methylation or protein expression level is not altered in expression, confirming that MMA sites contain regulated functions on their own. Collectively, we present a site-specific MMA dataset in human cells and demonstrate for the first time that MMA is a dynamic post-translational modification regulated during transcriptional arrest by a hitherto uncharacterized arginine demethylase. Data analysis: All raw data analysis was performed with MaxQuant software suite version 1.2.6.20 supported by the Andromeda search engine. Data was searched against a concatenated target/decoy (forward and reversed) version of the UniProtKB Human database encompassing 71,434 protein entries. Mass tolerance for searches was set to maximum 7 ppm for peptide masses and 20 ppm for HCD fragment ion masses. Data was searched with carbamidomethylation as a fixed modification and protein N-terminal acetylation, methionine oxidation and mono-methylation on lysine and arginine as variable modifications. A maximum of three mis-cleavages was allowed while requiring strict trypsin specificity, and only peptides with a minimum sequence length of seven were considered for further data analysis. Peptide assignments were statistically evaluated in a Bayesian model on the basis of sequence length and Andromeda score. Only peptides and proteins with a false discovery rate (FDR) of less than 1% were accepted, estimated on the basis of the number of accepted reverse hits. Protein sequences of common contaminants such as human keratins and proteases used were added to the database.
2019-11-25 | PXD000559 | Pride
Project description:Arginine methylation, Cob1. Wenya Hou et al Jena University Hospital
2018-04-30 | PXD008504 | Pride
Project description:Protein arginine methyltransferase 5 regulates AKT activation via methylation to promote metastasis
| PRJNA739706 | ENA
Project description:Therapeutic targeting of RNA splicing catalysis through inhibition of protein arginine methylation
| PRJNA509783 | ENA
Project description:PRMT1-dependent Arginine methylation regulates replication stress response through DNA-protein kinase
| PRJNA417451 | ENA
Project description:Protein arginine methyltransferases (PRMTs) catalyze arginine methylation, an abundant post-translational modification occurring on both chromatin-bound and cytoplasmic proteins. Growing evidence supports the involvement of PRMT5, the major Type II PRMT, in pro-survival and differentiation pathways, important during development and to promote tumorigenesis. Thus, PRMT5 emerges as an attractive drug target and inhibitors are currently in clinical trials for cancer therapy. However, the knowledge of PRMT5 non-histone substrates is still limited, as are the dynamic changes in methylation levels upon its inhibition. Here, we employed a newly established pipeline coupling SILAC with methyl-peptides immuno-enrichment to globally profile arginine methylation following PRMT5 inhibition by GSK591 and adopted the heavy-methyl SILAC as orthogonal validation method to reduce false discovery rate. Then, in vitro methylation assays on a set of PRMT5 targets provided novel mechanistic insights into its strict preference to methylate arginine sandwiched between two neighbouring glycines (GRG). In conclusion, we identified novel PRMT5 substrates, thus providing the first proof of concept of the in vivo efficacy of PRMT5 inhibitor that impacts on arginine methylation beyond histones.
2019-04-10 | PXD009070 | Pride