No abstract

Protein methylation is a common posttranslational modification that mostly occurs on arginine and lysine residues. Arginine methylation has been reported to regulate RNA processing, gene transcription, DNA damage repair, protein translocation, and signal transduction. Lysine methylation is best known to regulate histone function and is involved in epigenetic regulation of gene transcription. To better study protein methylation, we have developed highly specific antibodies against monomethyl arginine; asymmetric dimethyl arginine; and monomethyl, dimethyl, and trimethyl lysine motifs. These antibodies were used to perform immunoaffinity purification of methyl peptides followed by LC-MS/MS analysis to identify and quantify arginine and lysine methylation sites in several model studies. Overall, we identified over 1000 arginine methylation sites in human cell line and mouse tissues, and ∼160 lysine methylation sites in human cell line HCT116. The number of methylation sites identified in this study exceeds those found in the literature to date. Detailed analysis of arginine-methylated proteins observed in mouse brain compared with those found in mouse embryo shows a tissue-specific distribution of arginine methylation, and extends the types of proteins that are known to be arginine methylated to include many new protein types. Many arginine-methylated proteins that we identified from the brain, including receptors, ion channels, transporters, and vesicle proteins, are involved in synaptic transmission, whereas the most abundant methylated proteins identified from mouse embryo are transcriptional regulators and RNA processing proteins.

To ensure survival in the face of genomic insult, cells have evolved complex mechanisms to respond to DNA damage, termed the DNA damage checkpoint. The serine/threonine kinases ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR) activate checkpoint signaling by phosphorylating substrate proteins at SQ/TQ motifs. Although some ATM/ATR substrates (Chk1, p53) have been identified, the lack of a more complete list of substrates limits current understanding of checkpoint pathways. Here, we use immunoaffinity phosphopeptide isolation coupled with mass spectrometry to identify 570 sites phosphorylated in UV-damaged cells, 498 of which are previously undescribed. Semiquantitative analysis yielded 24 known and 192 previously uncharacterized sites differentially phosphorylated upon UV damage, some of which were confirmed by SILAC, Western blotting, and immunoprecipitation/ Western blotting. ATR-specific phosphorylation was investigated by using a Seckel syndrome (ATR mutant) cell line. Together, these results provide a rich resource for further deciphering ATM/ATR signaling and the pathways mediating the DNA damage response.DNA damage ͉ mass spectrometry ͉ phosphorylation M aintaining the integrity of the genome is of utmost importance for cellular survival. For this reason, cells have evolved complex mechanisms to inhibit cell cycle progression in response to genomic insult, termed the DNA damage checkpoint (1). Activating checkpoint mechanisms gives cells time to repair or bypass the damage using specialized DNA polymerases or, in cases of high levels of damage, to activate apoptotic pathways (2). Elucidating pathways involved in checkpoint activation and maintenance continues to be an active area of research.A family of phosphoinositol-3-phosphate kinase-like kinases are critical to the proper function of the DNA damage checkpoint. The two central kinases involved are ataxia telangiectasiamutated (ATM) and ATM and Rad3-related (ATR). This kinase family also includes DNA-dependent protein kinase (DNA-PK) and a more recently discovered member of the family, SMG1 (3). These kinases are activated in response to DNA damage and subsequently phosphorylate targets responsible for such diverse activities as blocking cell cycle progression, coordinating DNA repair activities, and affecting transcription of DNA damage response genes. ATR is activated in response to a variety of damaging agents: UV light, alkylating agents such as methyl methanesulfonate (MMS), and chemical inhibitors of DNA replication such as aphidicolin and hydroxyurea (4, 5). ATM, however, is primarily involved in the response to double-strand breaks, such as those caused by gamma irradiation (IR) (6). Deficiency in ATM/R, as well as other components of the DNA damage checkpoint, has been found to cause debilitating diseases such as ataxia telangiectasia (ATM mutants), Fanconi's anemia, Seckel syndrome (ATR mutants), and the avoidance of checkpoint activation to allow cancer progression.In response to DNA damage, ATM/R phosphorylate checkpoint k...

Growing interest in extracellular vesicles (EVs, including exosomes and microvesicles) as therapeutic entities, particularly in stem cell‐related approaches, has underlined the need for standardization and coordination of development efforts. Members of the International Society for Extracellular Vesicles and the Society for Clinical Research and Translation of Extracellular Vesicles Singapore convened a Workshop on this topic to discuss the opportunities and challenges associated with development of EV‐based therapeutics at the preclinical and clinical levels. This review outlines topic‐specific action items that, if addressed, will enhance the development of best‐practice models for EV therapies. Stem Cells Translational Medicine 2017;6:1730–1739