Downstream DNA selectively affects a paused conformation of human RNA polymerase II.
Transcriptional pausing by human RNA polymerase II (RNAPII) in the HIV-1 LTR is caused principally by a weak RNA:DNA hybrid that allows rearrangement of reactive or catalytic groups in the enzyme's active site. This rearrangement creates a transiently paused state called the unactivated intermediate that can backtrack into a more long-lived paused species. We report that three different regions of the not-yet-transcribed DNA just downstream of the pause site affect the duration of the HIV-1 pause, and also can influence pause formation. Downstream DNA in at least one region, a T-tract from +5 to +8, increases pause duration by specifically affecting the unactivated intermediate, without corresponding effects on the active or backtracked states. We suggest this effect depends on RNAPII-modulated DNA plasticity and speculate it is mediated by the "trigger loop" thought to participate in RNAP's catalytic cycle. These findings provide a new framework for understanding downstream DNA effects on RNAP.
Palangat
Murali
M
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Hittinger
Christopher T
CT
Landick
Robert
R
D001483:Base Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D002467:Cell Nucleus / Q000378:metabolism; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006367:HeLa Cells; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D012319:RNA Polymerase II / Q000737:chemistry*; D014158:Transcription, Genetic / Q000235:genetics
D004279:DNA, Viral; D009692:Nucleic Acid Heteroduplexes; D012319:RNA Polymerase II