The RAP74 subunit of human transcription factor IIF has similar roles in initiation and elongation

Transcription factor IIF (TFIIF) is a protein allosteric effector for RNA polymerase II during the initiation and elongation phases of the transcription cycle. In initiation, TFIIF induces promoter DNA to wrap almost a full turn around RNA polymerase II in a complex that includes the general transcription factors TATA-binding protein, TFIIB, and TFIIE. During elongation, TFIIF also supports a more active conformation of RNA polymerase II. This conformational model for elongation is supported by three lines of experimental evidence. First, a region within the RNA polymerase II-associating protein 74 (RAP74) subunit of TFIIF (amino acids T154 to M177), a region that is critical for isomerization of the preinitiation complex, is also critical for elongation stimulation. Amino acid substitutions within this region are shown to have very similar effects on initiation and elongation, and mutagenic analysis indicates that L155, W164, N172, I176, and M177 are the most important residues in this region for transcription. Second, TFIIF is shown to have a higher affinity for rapidly elongating RNA polymerase II than for the stalled elongation complex, indicating that RNA polymerase II alternates between active and inactive states during elongation and that TFIIF stimulates elongation by supporting the active conformational state of RNA polymerase II. The deleterious I176A substitution in the critical region of RAP74 decreases the affinity of TFIIF for the active form of the elongation complex. Third, TFIIF is shown by Arrhenius analysis to stimulate elongation by populating an activated state of RNA polymerase II.