A highly purified RNA polymerase II elongation control system

Studying the sensitivity of transcription to the nucleotide analog 5,6-dich loro-1-beta -D-ribofuranosylbenzimidazole has led to the discovery of a num ber of proteins involved in the regulation of transcription elongation by R NA polymerase II. We have developed a highly purified elongation control sy stem composed of three purified proteins added back to isolated RNA polymer ase II elongation complexes. Two of the proteins, 5,6-dichloro-1-13D-ribofu ranosylbenzimidazole sensitivity-inducing factor (DSIF) and negative elonga tion factor (NELF), act as negative transcription elongation factors by inc reasing the time the polymerase spent at pause sites. reverses the negative effect of DSIF and NELF through a mechanism dependent on its kinase activi ty. TFIIF is a general initiation factor that positively affects elongation by decreasing pausing. We show that TFIIF functionally competes with DSIF and NELF, and this competition is dependent on the relative concentrations of TFIIF and NELF.