Human Arginine Methylome
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Michael Lund Nielsen
PROVIDER: MSV000080836 | MassIVE | Fri Mar 31 18:24:00 BST 2017
SECONDARY ACCESSION(S): PXD003700
REPOSITORIES: MassIVE
Publications
Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells.
Larsen Sara C SC Sylvestersen Kathrine B KB Mund Andreas A Lyon David D Mullari Meeli M Madsen Maria V MV Daniel Jeremy A JA Jensen Lars J LJ Nielsen Michael L ML
Science signaling 20160830 443
The posttranslational modification of proteins by arginine methylation is functionally important, yet the breadth of this modification is not well characterized. Using high-resolution mass spectrometry, we identified 8030 arginine methylation sites within 3300 human proteins in human embryonic kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are le ...[more]
Similar Datasets
Project description:Identification of arginine methylation sites in human HEK293 cells, yielding a total of >8.000 high-confident modification sites on >3.300 proteins
2016-09-30 | PXD003700 | Pride
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:Methylation is a common post-translational modification of lysine and arginine in eukaryotic proteins. To date, these methylomes are best characterised in model organisms and higher eukaryotes. Herein, we integrated bioinformatics, proteomics and high-content drug-screening to comprehensively explore protein methylation in the human gastrointestinal parasite and deep-branching eukaryote, Giardia duodenalis. We demonstrate Giardia and other Diplomonadida species lack arginine-methyltransferases and have remodelled RGG/RG motifs preferred by these enzymes. Further, Giardia had no detectable methylarginine in vitro, demonstrating the first eukaryote with no arginine methylome. In contrast, we performed detailed curation of 11 putative lysine-methyltransferases, including highly-diverged SET-domain proteins, and novel annotations demonstrating conserved eEF1a methyllysine. We identified >200 high-confidence methyllysine sites, highlighting methyllysine within coiled-coil features, and for Giardia cytoskeletal regulation. Lastly, using known methylation-inhibitors, we demonstrate inhibition of methylation plays a key role in replication and cyst formation in this parasite.
2020-08-07 | PXD016813 | Pride
Project description:Reversible protein phosphorylation is an important and ubiquitous protein modification in all living cells. We report that protein arginine phosphorylation plays a physiological significant role for the regulation of protein activity. We detected 121 arginine phospho-sites for 87 proteins in the Gram-positive model organism Bacillus subtilis in vivo. Moreover, we provide evidences that arginine phosphorylations are involved in the fine-tuned signal transduction of many critical cellular processes, such as protein degradation, motility, competence, stringent and stress response. Our results suggest that in B. subtilis the activity of a protein arginine phosphatase allows a fast regulation of protein activity by protein arginine kinases and that protein arginine phosphorylations play an important role as a reversible post-translational modification in bacteria. Cells were grown under vigorous agitation at 37 M-BM-0C in a defined medium (StM-CM-<lke et al., 1993, J Gen Microbiol 139, 2041-2045). Samples were taken at OD500 0.4 and 1h upon entry into stationary phase. Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.
2012-03-31 | E-GEOD-31249 | biostudies-arrayexpress
Project description:Arginine methylation of METTL14 promotes RNA N6-methyladenosine modification
| PRJNA688706 | ENA
Project description:Reversible protein phosphorylation is an important and ubiquitous protein modification in all living cells. We report that protein arginine phosphorylation plays a physiological significant role for the regulation of protein activity. We detected 121 arginine phospho-sites for 87 proteins in the Gram-positive model organism Bacillus subtilis in vivo. Moreover, we provide evidences that arginine phosphorylations are involved in the fine-tuned signal transduction of many critical cellular processes, such as protein degradation, motility, competence, stringent and stress response. Our results suggest that in B. subtilis the activity of a protein arginine phosphatase allows a fast regulation of protein activity by protein arginine kinases and that protein arginine phosphorylations play an important role as a reversible post-translational modification in bacteria.
2012-04-01 | GSE31249 | 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:The formation of condensates in membraneless organelles is thought to be driven by protein phase separation. Arginine methylation and serine/threonine phosphorylation are important in the phase separation process, however these post-translational modifications are often present in intrinsically disordered regions that are difficult to analyse with standard proteomic techniques. Here we use a multi-protease and multi-MS/MS fragmentation approach, coupled with heavy methyl SILAC and phospho- or methyl-peptide enrichment, for the analysis of arginine methylation and serine/threonine phosphorylation, and to understand their co-occurrence in condensate-associated proteins. For Saccharomyces cerevisiae, we report a 50% increase in the known arginine methylproteome, involving 15 proteins that are almost all condensate-associated. Importantly, some of these proteins have arginine methylation on all predicted sites – providing evidence that this modification can be pervasive. We explored whether arginine methylated condensate-associated proteins are also phosphorylated, and found 12 such proteins to carry phosphoserine or phosphothreonine. In Npl3, Ded1 and Ssbp1, single peptides were found to carry both modifications, indicating a co-occurrence in close proximity and on the same protein molecule. We show that these co-modifications occur in regions of disorder and that arginine methylation is typically on basic regions of disorder. For phosphorylation, its association with charged regions of condensate-associated proteins was less consistent, although some regions with multisite phosphorylation sites were strongly acidic. We conclude that arginine-methylated proteins associated with condensates are typically co-modified with protein phosphorylation.
2021-09-17 | PXD022403 | 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 C-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit POLR2A is a platform for modifications specifying the recruitment of factors that regulate transcription, mRNA processing, and chromatin remodeling. Here, we show that a CTD arginine residue (R1810 in human) that is conserved across vertebrates is symmetrically dimethylated (me2s). This R1810me2s modification requires Protein Arginine Methyltransferase 5 (PRMT5) and recruits the Tudor domain of the Survival of Motor Neuron (SMN) protein, which is mutated in spinal muscular atrophy (SMA). SMN interacts with Senataxin, which is sometimes mutated in Ataxia Oculomotor Apraxia 2 (AOA2) and Amyotrophic Lateral Sclerosis (ALS4). Because R1810me2s and SMN, like Senataxin, are required for resolving RNA-DNA hybrids, created by RNA polymerase II, that form â??R-loopsâ?? in transcription termination regions, we propose that R1810me2s, SMN, and Senataxin are components of a pathway for R-loop resolution in which defects can influence transcription termination and may contribute to neurodegenerative disorders. ChIP of RNAPII in Raji cells expressing shRNG against SMN or GFP; ChIP against RNAPII in Raji cells where endogenous RNAPII has been replaced with wt or R1810A mutant amanitin-resistant protein; and ChIP of SMN in HEK293 cells.
2015-12-31 | E-GEOD-73379 | biostudies-arrayexpress