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PRMT1-mediated methylation regulates MLL2 stability and gene expression

ABSTRACT: The interplay between multiple transcription factors precisely regulates eukaryotic transcription. Here, we report that the protein methyltransferases, MLL2 and PRMT1, interact directly and act collectively to regulate gene expression. PRMT1 binds to the N-terminal region of MLL2, considered an intrinsically disordered region, and methylates multiple arginine residues within its RGG/RG motifs. Notably, overexpression of PRMT1 decreased poly-ubiquitylation of MLL2, whereas mutations on methylation sites in MLL2 increased MLL2 poly-ubiquitylation, suggesting that PRMT1-mediated methylation stabilizes MLL2. MLL2 and PRMT1 cooperatively stimulated the expression of a chromosomal reporter gene in a PRMT1-mediated, MLL2-methylation–dependent manner. RNA-seq analysis found that MLL2 and PRMT1 jointly regulate the expression of genes involved in cell membrane and extracellular matrix functions, and depletion of either resulted in impaired cell migration and invasion. Our study provides evidence that PRMT1-mediated MLL2 methylation regulates MLL2 protein stability and the expression of their target genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE274754 | GEO | 2024/10/21

REPOSITORIES: GEO

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Project description:PRMT5 is the major enzyme that catalyzes the symmetric dimethylation of arginine (sDMA) in mammalian cells. Its activity is crucial for many biological processes including transcriptional regulation, mRNA processing, as well as DNA damage and repair. However, the protein substrates identified for PRMT5 have yet been limited in numbers, hindering the understanding of PRMT5 functions in normal as well as diseased cells. Herein we developed an optimized strategy for proteomic profiling of cellular sDMA and apply it to the discovery of novel PRMT5 substrates. Our results show that a combination of proteolytic digestion by the metalloprotease ulilysin and using electron-transfer dissociation with supplemental activation as the mass spectrometry method significantly increased sDMA site identification and localization after immuno-affinity enrichment. By employing SILAC-based differential quantitative proteomic approach and a PRMT5 specific inhibitor, we identified 325 sDMA sites being regulated by PRMT5, 220 being novel sites, which greatly expanded the number of PRMT5 substrates. Biochemical studies confirmed the newly discovered PRMT5 substrate, Plasminogen activator inhibitor 1 RNA-binding protein (SERBP1) and revealed that the RGG/RG motif in the central region of SERBP1 contains both PRMT5-catalyzed sDMA and Type I PRMT-catalyzed asymmetric dimethylation of arginine (aDMA). Unexpectedly, using the optimized methylarginine profiling strategy, we also discovered arginine trimethylation, a previously unknown type of modification, on the central RGG/RG region of SERBP1. By mutational studies we demonstrated that the trimethyl modification on R172 of SERBP1 regulates its recruitment to stress granule (SG) under oxidative stress, indicating a functional role of arginine trimethylation in the cell. Overall, the optimized profiling strategy not only enabled the identification of extensive, non-overlapping sDMA sites and novel PRMT5 substrates, but also revealed a potentially important new PTM, arginine trimethylation. The work lays the foundation for further investigations on the functional interplay of different methylation modifications on arginines, especially in the heavily methylated RGG/RG motif of many RNA-binding proteins.

Project description:Somatic mutations of the MLL2 methyltransferase gene represent a common genetic lesion in multiple cancer types. In diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL) (collectively, over 70% of all lymphoma diagnoses), these mutations are highly recurrent and appear early during transformation, possibly in pre-malignant precursors. Here we show that FL- and DLBCL-associated MLL2 mutations impair its enzymatic activity and lead to diminished global H3K4 methylation in normal germinal-center (GC) B cells and DLBCL, consistent with the enrichment of MLL2 binding at enhancer and promoter regions marked by mono- and tri-methylation. Conditional deletion of Mll2 early during B cell development, but not after initiation of the GC reaction, leads to increased percentages and numbers of GC B cells, which feature a distinct transcriptional profile defined by the enrichment of cell-cycle regulatory and B-cell receptor signaling genes. Consistently, Mll2-deficient B cells exhibit proliferative advantage and accumulation in the S phase of the cell cycle, which is influenced by the number of cell divisions. While GC-specific loss of Mll2 was not sufficient to initiate malignant transformation, compound Mll2-deficient/BCL2-transgenic mice displayed an increased incidence of clonal lymphoproliferations resembling the features of human FL and DLBCL. These findings suggest that early MLL2 loss favors BCL2-induced lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cells. Eradication of MLL2-deficient cells may represent a rational therapeutic approach targeting early tumorigenic events. Murine germinal center B cells (B220+CD95+PNA+) were sorted from the spleen of conditional Mll2 knock-out, Mll2 heterozygous and Mll2 wild type mice (crossed with CD19-Cre or Cg1-Cre deletor strains) and sacrificed at day 12 after immunization with sheep red blood cells (SRBC)(n=3 mice per genotype). Total RNA was extracted from single cell suspensions and processed according to the Ovation RNA Amplification System and Encore® Biotin Module protocols (both from NuGEN). Samples were analyzed on Affymetrix Mouse Genome 430 2.0 arrays.

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PRMT1-mediated methylation regulates MLL2 stability and gene expression

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