Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth

Wen-Juan Li,Guo-Sheng Hu,Helen He Zhu,Jing-Jing Yang,Wen Liu,Yi-An Lin,Hai-Hua Huang,Yao-Hui He,Bing-Lan Xie,Bing-Ling Peng,Feng Ye,Ting Ran,Ming-Feng Huang,Xiang Gao

doi:10.1038/s41467-021-21963-1

Abstract

Numerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). However, the full substrate spectrum of the only type III PRMT, PRMT7, and its connection to type I and II PRMT substrates remains unknown. Here, we use mass spectrometry to reveal features of PRMT7-regulated methylation. We find that PRMT7 predominantly methylates a glycine and arginine motif; multiple PRMT7-regulated arginine methylation sites are close to phosphorylations sites; methylation sites and proximal sequences are vulnerable to cancer mutations; and methylation is enriched in proteins associated with spliceosome and RNA-related pathways. We show that PRMT4/5/7-mediated arginine methylation regulates hnRNPA1 binding to RNA and several alternative splicing events. In breast, colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Pharmacological inhibition of PRMT4/5/7 suppresses cancer cell growth and their co-inhibition shows synergistic effects, suggesting them as targets for cancer therapy.

Highlights

Numerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs)
human embryonic kidney 293 (HEK293) cells were transfected with control siRNA and siRNA specific targeting PRMT7 followed by immunoblotting analysis with antimono-methyl-arginine (MMA), asymmetric di-methyl-arginine, or symmetric di-methyl-arginine-specific antibodies
Knockdown of PRMT7 led to a significant decrease in MMA but not in asymmetric di-methylarginine (aDMA) or symmetric di-methyl-arginine (sDMA), which was consistent with previous reports showing that the predominant activity of PRMT7 is the mono-methylation of arginine residues in proteins (Fig. 1a)[36,37,38]

Summary

Introduction

Numerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). Colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Arginine methylation was first discovered in the early 1970s3,4 and was later recognized as a widespread posttranslational modification (PTM) in many proteins[5,6,7,8] It plays important roles in signaling transduction, DNA damage repair, gene transcription, splicing regulation, and RNA metabolism, among others[9]. Owing to the functional importance of arginine methylation in many proteins, PRMTs have been reported to be involved in the transcriptional and post-transcriptional regulation of gene expression, mRNA processing and translation, and intracellular signaling during development and disease progression, in cancers[10,11]. The function of PRMTs in both physiological and pathological conditions is often dependent on their methyltransferase activity

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Conclusion