Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism.

The adenovirus major late arrest site blocks transcription by mammalian RNA polymerase II in vitro downstream of the major late promoter but not the mouse beta-globin promoter. We localized the sequences responsible for anti-arrest to the 5' end of the beta-globin transcript and demonstrated that anti-arrest required that this region of RNA form base pairs with the nascent transcript upstream of the arrest site. Small antisense RNA or DNA oligonucleotides hybridizing upstream of the arrest site also prevented arrest when added in trans. Our results suggest that arrest is accompanied by retraction of the nascent transcript into the interior of the polymerase and that hybridization of the transcript prevents this movement, thereby allowing the polymerase to continue elongation.