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.