hRPB9 is a subunit unique to RNA polymerase II, although it has sequence homologues in RNA polymerases I and III. The gene for Rpb9 is not essential for yeast cell viability, but is essential in Drosophila. hRPB9 has roles in both transcription initiation and transcription elongation. In the initiation reaction it is necessary for accurate start site selection. In the elongation reaction, RPB9, along with TFIIS facilitates the conversion of an arrest-competent conformation to a read-through competent conformation. RNA polymerase II lacking the RPB9 subunit uses alternate transcription initiation sites in vitro and in vivo and is unable to respond to the transcription elongation factor TFIIS in vitro. A role in the modulation of initiation and elongation is consistent with the localization of RPB9 in the three-dimensional structure of yeast RNA polymerase II. RPB9 is located at the tip of the so-called "jaws" of the enzyme, which is thought to function by clamping the DNA downstream of the active site. RPB9 comprises two zinc ribbon domains joined by a conserved linker region. The C-terminal zinc ribbon is similar in sequence to that found in TFIIS.

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