Eukaryotic nuclei house three distinct RNA polymerases, which can be separated using ion-exchange chromatography. RNA polymerase I resides in the nucleolus, while other two are located in the nucleoplasm. Each of these polymerases performs specific transcriptional roles. Polymerase I synthesizes a large precursor to the major rRNAs (5.8S, 18S, and 28S in vertebrates). Polymerase II generates hnRNAs, precursors to mRNAs, as well as miRNA precursors and most small nuclear RNAs (snRNAs). Polymerase III is responsible for producing precursors of 5S rRNA, tRNAs, and various other small cellular and viral RNAs.

The subunit structures of the three nuclear polymerases have been analyzed in several eukaryotes, revealing multiple subunits, including two large ones exceeding 100 kD in molecular mass. Common subunits appear in all three polymerases across eukaryotes. In yeast, the genes encoding all 12 RNA polymerase II subunits have been sequenced and subjected to mutation analysis. Among these subunits, three resemble the core subunits of bacterial RNA polymerases in structure and function, five are shared by all three nuclear polymerases, two are dispensable under normal conditions, and two do not fit into these categories.

Subunit IIa, the primary product of the yeast RPB1 gene, can be converted to IIb in vitro through the proteolytic removal of the carboxyl-terminal domain (CTD), which consists of repeated heptapeptides. In vivo, subunit IIa is phosphorylated at two serines within the CTD heptad to form IIo. The enzyme containing the IIa subunit (polymerase IIA) binds to the promoter, while the enzyme with the IIo subunit (polymerase IIO) participates in transcript elongation.

The structure of yeast pol II D4/7 reveals a deep cleft capable of accommodating a DNA template. The catalytic activity and functional mechanisms of these polymerases underscore their critical roles in eukaryotic transcription.