Tadahiro Shimazu1,7, Rei Yoshimoto2,7, Kaoru Kotoshiba1, Takehiro Suzuki3, Shogo Matoba4, Michiko Hirose4, Mai Akakabe5,6, Yoshihiro Sohtome5,6, Mikiko Sodeoka5,6, Atsuo Ogura4, Naoshi Dohmae3 and Yoichi Shinkai1 1Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; 2Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan; 3Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; 4Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan; 5Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; 6RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan Corresponding authors: yshinkairiken.jp, tshimazuriken.jp

↵7 These authors contributed equally to this work.

Abstract

Histidine (His) residues are methylated in various proteins, but their roles and regulation mechanisms remain unknown. Here, we show that carnosine N-methyltransferase 1 (CARNMT1), a known His methyltransferase of dipeptide carnosine (βAla-His), is a major His N1-position-specific methyltransferase. We found that 52 His sites in 20 proteins underwent CARNMT1-mediated methylation. The consensus methylation site for CARNMT1 was identified as Cx(F/Y)xH, a C3H zinc finger (C3H ZF) motif. CARNMT1-deficient and catalytically inactive mutant mice showed embryonic lethality. Among the CARNMT1 target C3H ZF proteins, RNA degradation mediated by Roquin and tristetraprolin (TTP) was affected by CARNMT1 and its enzymatic activity. Furthermore, the recognition of the 3′ splice site of the CARNMT1 target C3H ZF protein U2AF1 was perturbed, and pre-mRNA alternative splicing (AS) was affected by CARNMT1 deficiency. These findings indicate that CARNMT1-mediated protein His methylation, which is essential for embryogenesis, plays roles in diverse aspects of RNA metabolism by targeting C3H ZF-type RNA-binding proteins and modulating their functions, including pre-mRNA AS and mRNA degradation regulation.

Received April 28, 2023. Accepted August 2, 2023.