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Comprehensive transcriptome analysis of the brain in CNS-specific PRMT1 knockout mice.

ABSTRACT: Arginine methylation is a common post-translation modification that is catalyzed by protein arginine methyltransferases (PRMTs). We generated the central nervous system-specific PRMT1 deficient (PRMT1-CKO) mice by Cre-loxP recombination system. Recently, we have discovered that PRMT1 is essential for development of CNS, and it is especially crucial for oligodendrocyte lineage progression and the subsequent myelination. In this study, we performed a comprehensive analysis of gene expression changes in whole brains, cortices or cerebella of wild type (WT) and PRMT1-CKO mice using RNA sequencing (RNA-seq). Filtering characteristics were used to identify the differentially expressed genes using the CLC Genomics Workbench software

ORGANISM(S): Mus musculus

PROVIDER: GSE126127 | GEO | 2020/08/14

REPOSITORIES: GEO

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Project description:Protein methylation has been implicated in many important biological contexts including signaling, metabolism, and transcriptional control. Despite the importance of this post- translational modification, the global analysis of protein methylation by mass spectrometry-based proteomics has not been extensively studied due to the lack of robust, well-characterized techniques for methyl-peptidemethyl peptide enrichment. Here, to better investigate protein methylation, we optimized and compared two methods for methyl-peptidemethyl peptide enrichment: immunoaffinity purification (IAP) and high pH strong cation exchange (SCX). Comparison of these methods revealed that they are largely orthogonal for monomethyl arginine (MMA), suggesting that the usage of both techniques is required to provide a global view of protein methylation. Using both IAP and SCX, we investigated changes in protein methylation downstream of protein arginine methyltransferase 1 (PRMT1). Together, these techniques allowed us to quantify over ~1,000 arginine methylation sites on 407 proteins. Of these methylation sites, PRMT1 knockdown resulted in significant changes to 110 arginine methylation sites on 59 proteins. In contrast, zero lysine methylation sites were significantly changed upon PRMT1 knockdown. In PRMT1 knockdown cells, 24 MMA sites exhibited both significant downregulation (ie, putative PRMT1-mediated MMA targets) and 63 significant upregulation (ie, putative PRMT1-mediated ADMA targets). PRMT1 knockdown induced significant changes in asymmetric dimethyl arginine (ADMA), consistent with being PRMT1 targets. Additionally, We also observed that PRMT1 knockdown induced significant increases in symmetric dimethyl arginine (SDMA) methylation, suggesting that loss of PRMT1 activity allows scavenging of PRMT1 substrates by Type II PRMTs. Analysis of the subcellular localization and protein function of the significantly changing methyl-proteins revealed that the majority of PRMT1 substrates are localized to the nucleus and involved in RNA and DNA binding. Taken together, our results suggest that deep protein methylation profiling by mass spectrometry requires orthogonal enrichment techniques, identify novel PRMT1 methylation targets, and highlight in order to understand the dynamic interplay between methyltransferases in mammalian cells.

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Comprehensive transcriptome analysis of the brain in CNS-specific PRMT1 knockout mice.

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