Identification and purification of a yeast protein that affects elongation by RNA polymerase II

We have purified from whole cell extracts of Saccharomyces cerevisiae a protein which alters the elongation properties of yeast RNA polymerase II in vitro. The yeast elongation stimulatory activity, YES, correlates with a 116-kDa protein and acts on both yeast and Drosophila RNA polymerase II during transcription of double-stranded dC-tailed templates. The stimulatory activity is specific for RNA polymerase II since it has no significant effect on the elongation properties of yeast RNA polymerase I or yeast RNA polymerase III. Elongation by RNA polymerase II can be stimulated by RNase H on dC-tailed templates; however, the stimulatory activity of YES is not due to RNase H activity. YES does not stimulate RNA polymerase II in the presence of manganese ions and therefore is distinct from the smaller elongation factor, S-II or DmS-II. YES is most similar to Drosophila factor 5 (mammalian TFIIF, or RAP30/74), an initiation factor that is also able to increase the rate of elongation of RNA polymerase II.