A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS

doi:10.1073/pnas.0409405102

A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS

^*Department of Bacteriology, University of Wisconsin, Madison, WI 53706; and ^†Department of Biochemistry, University of Iowa, Iowa City, IA 52242

Edited by Jeffrey W. Roberts, Cornell University, Ithaca, NY, and approved August 9, 2005 (received for review December 16, 2004)

Abstract

Formation of productive transcription complexes after promoter escape by RNA polymerase II is a major event in eukaryotic gene regulation. Both negative and positive factors control this step. The principal negative elongation factor (NELF) contains four polypeptides and requires for activity the two-polypeptide 5,6-dichloro-1-β-d-ribobenzimidazole-sensitivity inducing factor (DSIF). DSIF/NELF inhibits early transcript elongation until it is counteracted by the positive elongation factor P-TEFb. We report a previously undescribed activity of DSIF/NELF, namely inhibition of the transcript cleavage factor TFIIS. These two activities of DSIF/NELF appear to be mechanistically distinct. Inhibition of nucleotide addition requires ≥18 nt of nascent RNA, whereas inhibition of TFIIS occurs at all transcript lengths. Because TFIIS promotes escape from promoter-proximal pauses by stimulating cleavage of back-tracked nascent RNA, TFIIS inhibition may help DSIF/NELF negatively regulate productive transcription.

Footnotes

↵ ‡ To whom correspondence should be addressed. E-mail: landick{at}bact.wisc.edu.
Author contributions: M.P., D.H.P., and R.L. designed research; M.P. performed research; D.B.R. and D.H.P. contributed new reagents/analytic tools; M.P. and R.L. analyzed data; and R.L. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: DSIF, 5,6-dichloro-1-β-D-ribobenzimidazole-sensitivity inducing factor; NELF, negative elongation factor; RNAPII, RNA polymerase II; TEC, transcription elongation complex; CTD, C-terminal heptapeptide repeat domain.