Eukaryotes have three RNA polymerases, designated I, II, and III, which are distinct complexes but have certain subunits in common. Each polymerase has a specific function and is recruited to a specific promoter sequence.

RNA polymerase I (Pol I) is responsible for the synthesis of only one type of RNA, a transcript called preribosomal RNA (or pre-rRNA), which contains the precursor for the 18S, 5.8S, and 28S rRNAs. Pol I promoters differ greatly in sequence from one species to another.

The principal function of RNA polymerase II (Pol II) is synthesis of mRNAs and some specialized RNAs. This enzyme can recognize thousands of promoters that vary greatly in sequence. Some Pol II promoters have a few sequence features in common, including a TATA box (eukaryotic consensus sequence TATA(A/T)A(A/T)(A/G)) near base pair −30 and an Inr sequence (initiator) near the RNA start site at +1. However, such promoters are in the minority, and elaborate interactions with regulatory proteins guide Pol II function at many promoters that lack these features.

RNA polymerase III (Pol III) makes tRNAs, the 5S rRNA, and some other small specialized RNAs. The promoters recognized by Pol III are well characterized. Some of the sequences required for the regulated initiation of transcription by Pol III are located within the gene itself, whereas others are in more conventional locations upstream of the RNA start site.