Transcriptome analysis of CARNMT1 knockout tissue
Histidine (His) residues are methylated in various proteins, but their roles and regulation mechanisms remain unknown. Here, we showed that CARNMT1, a known His methyltransferase of dipeptide carnosine (ßAla-His), is the major protein His N-position-specific methyltransferase. ProSeAM labeling and proteomic analysis revealed that 52 His sites in 20 proteins underwent CARNMT1-mediated methylation. The consensus methylation site for CARNMT1 was identified as Cx(F/Y)xH, which is 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 TTP was affected by CARNMT1 and its enzymatic activity. Furthermore, splicing factor, U2AF1's 3'-splice site recognition was perturbed and pre-mRNA alternative splicing (AS) was also 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 regulation of mRNA degradation. Overall design: Examination of transcriptome of CARNMT1 knockout mice by Ribosomal RNA depleted RNA-Seq