N^6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation

N⁶-Methyladenosine (m⁶A) RNA modification is present in messenger RNAs (mRNA), ribosomal RNAs (rRNA), and spliceosomal RNAs (snRNA) in humans. Although mRNA m⁶A modifications have been extensively studied and shown to play critical roles in many cellular processes, the identity of m⁶A methyltransferases for rRNAs and the function of rRNA m⁶A modifications are unknown. Here we report a new m⁶A methyltransferase, ZCCHC4, which primarily methylates human 28S rRNA and also interacts with a subset of mRNAs. ZCCHC4 knockout eliminates m⁶A4220 modification in 28S rRNA, reduces global translation, and inhibits cell proliferation. We also find that ZCCHC4 protein is overexpressed in hepatocellular carcinoma tumors, and ZCCHC4 knockout significantly reduces tumor size in a xenograft mouse model. Our results highlight the functional significance of an rRNA m⁶A modification in translation and in tumor biology.