Saccharomyces cerevisiae RNA polymerase II conditional mutants that selectively disrupt the synthesis of specific mRNAs were isolated. At the permissive temperature, several of the mutants were inositol auxotrophs as a result of inadequate induction of INO1 transcription. The transcriptional defects exhibited by one of these Ino-mutants (rpb2-2) were further investigated. The induction of GAL1O and HIS4 transcription in rpb2-2 strains was similar to that of wild-type strains, in contrast to the lack of induction of INOI transcription. When shifted to the nonpermissive temperature, cells containing rpb2-2 continued to accumulate some mRNAs but not others. Together, these results indicate that transcription of specific genes can be disrupted by RNA polymerase II mutations. The rpb2-2 allele alters an amino acid residue that occurs in a highly conserved segment of the RPB2 protein and that is shared by homologous subunits in other species.The regulation of eucaryotic gene expression occurs primarily at the level of selective transcription initiation by RNA polymerase II. Specific promoter sequences, transcriptional activating protein factors, and RNA polymerase all play a role in transcription initiation. Transcriptional activating proteins bind specifically to cis-acting promoter elements such as enhancer sequences or the TATA box (12, 21). The most thoroughly studied transcriptional activating proteins have separate domains for DNA-binding and transcriptional activation (reviewed in references 13 and 22). The mechanism(s) by which these proteins activate transcription initiation by RNA polymerase II is unclear.RNA polymerase II is composed of 9 to 14 polypeptides of 10 to 220 kilodaltons that are substantially conserved in size and structure throughout eucaryotes (31). The yeast nuclear RNA polymerases are among the best studied of the eucaryotic polymerases. Yeast RNA polymerase II contains 10 polypeptides, 7 of which are unique to the enzyme and 3 of which are shared with the other two polymerases. Genes encoding seven of the yeast RNA polymerase II subunits have been isolated and characterized (17,18,29,(35)(36)(37); N. A. Woychik, S.-M. Liao, P. Kolodziej, and R. A. Young, Genes Dev., in press). The sequences of the two largest subunits, RPBJ and RPB2 (1,35), reveal that the RPB1 and RPB2 proteins are similar to the Escherichia coli RNA polymerase subunits P' (RpoC) and 1 (RpoB), respectively.Biochemical and genetic evidence indicates that the RNA polymerase ,B subunit interacts with the a subunit, which is essential for selective transcription initiation in E. coli (9,26,32,38). It is not clear how components of the eucaryotic RNA polymerase interact with transcription factors.To obtain clues to the functions of the RPBI and RPB2 subunits, we have isolated and investigated RNA polymerase mutants that affect mRNA synthesis. We previously described a temperature-sensitive RPBJ mutant that rapidly ceases all mRNA synthesis upon transfer to the nonpermis-