Host cell and virus-specific poly(A)-containing RNAs isolated from nuclei and cytoplasm of monkey kidney cells infected with simian virus 40 contain different methylated nucleotides. In the cytoplasmic simian virus 40-specific RNA, about 75% of the radioactivity derived from [methyl-3Hjmethionine was in N6-methyladenosine (N6mA) after digestion with Penicillium nuclease and bacterial alkaline phosphatase. The remainder was in a negatively charged component with properties of 5'-terminal structures, i.e., digestion with nucleotide pyrophosphatase and bacterial alkaline phosphatase released 2'-O-methyladenosine (Am), 2'-O-methylguanosine (Gm), and 7-methylguanosine (m7G), consistent with a 5'-terminal structure of the type, m7GpppNm. The nuclear virus-specific RNA contained N6mA, Gm, 2'-Omethyluridine (Um), and a smaller proportion (10%) of nuclease-, phosphatase-resistant presumptive 5' termini that also yielded Am, Gm, and m7G upon further hydrolysis. The infected cell nuclear and cytoplasmic RNAs that did not hybridize to DNA of simian virus 40 contained all four 2'-O-methylnucleosides. The possible role of methylation in the processing and translation of simian virus 40-specific mRNA is discussed.Methylation of mammalian cell mRNA is a recently recognized phenomenon (1, 2). It has been suggested that the maturation of cytoplasmic mRNAs, possibly via processing of heterogeneous nuclear RNA, may require RNA methylation (3). Although all animal cell mRNAs may not be derived by cleavage of larger precursors (4, 5), post-transcriptional methylation and processing of other types of cellular RNA, including ribosomal and transfer RNA, are well known (6).In addition to a possible intracellular role in the processing of RNA, methylation is also involved in the synthesis and function of several viral mRNAs that apparently are monocistronic genome transcripts and not derived from larger molecules. They include the mRNAs of cytoplasmic polyhedrosis virus (7), reovirus (8), vaccinia virus (9, 10), and vesicular stomatitis virus (11). All are specifically methylated at the 5' termini and contain structures of the type, m7G-(5')ppp(5')Nm. Furthermore, initiation of mRNA of cytoplasmic polyhedrosis virus in vitro by the virion-associated RNA polymerase requires the presence of the methyl donor, S-adenosylmethionine, and is coupled to methylation of the nascent RNA chains (12). Methylation of these viral mRNAs appears to be obligatory for their function, since translation of mRNAs of reovirus and vesicular stomatitis virus in cell-free extracts is completely dependent upon methylation of the mRNAs (13).Because of its probable biological significance, it is of interest to study methylation of specific mRNAs in eukaryotic cells. Simian virus 40 (SV40)-specific mRNAs can be isolated from cells by DNA. RNA hybridization, and information is available on viral transcription in both lytically infected and virus-transformed cells (14-16). In the nuclei of infected BSC-1 monkey cells the SV40 genome is symmetrically copied, and ...