Promoter clearance by RNA polymerase II

Abstract

Many changes must occur to the RNA polymerase II (pol II) transcription complex as it makes the transition from initiation into transcript elongation. During this intermediate phase of transcription, contact with initiation factors is lost and stable association with the nascent transcript is established. These changes collectively comprise promoter clearance. Once the transcript elongation complex has reached a point where its properties are indistinguishable from those of complexes with much longer transcripts, promoter clearance is complete. The clearance process for pol II consists of a number of steps and it extends for a surprisingly long distance downstream of transcription start. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

Fig. 1. Important stages in the progress of pol II to promoter clearance

The downstream progress of the pol II transcription bubble from the initial open complex to the completely cleared elongation complex is shown schematically. RNA is in red and the transcript length for that stage is indicated. This diagram is based on results obtained in mammalian systems with TATA box promoters. Only a very limited number of different promoters and initially transcribed regions have been investigated. (A) The location of the upstream edge of the bubble is determined by distance from the TATA element [15,16]; the initiation site remains double-stranded [14]. (B) Initiation is abortive and transcription can proceed for many rounds if RNA synthesis is limited to 2–3 nt [14,21,22]. (C) The RNA-DNA hybrid reaches its mature length and the structure of the hybrid is normal at this point [35,36]. The upstream edge of the bubble remains in its initial location as the leading edge advances [14,16]. Loss of transcripts through the abortive pathway is considerably reduced [14,27]. Transcript slippage within repeated template segments falls off abruptly just downstream of this point [34]. Nascent RNA should begin to clash with the finger/reader segment of TFIIB just upstream of this point [44]. (D) At this point, roughly the upstream half of bubble closes abruptly as the unpaired region extends to ~18 bases [14,16]. For a promoter with the canonical spacing of the TATA box and transcription start, this occurs at a transcript length of 9–10 nt [16]. TFIIH is no longer required for effective elongation [16]. Loss of an upstream contact of TFIIB with the template has been proposed to occur here [5]. (E) TFIIB is destabilized within the advancing complex [22]. (F) As elongation continues, the 5’ end of the nascent RNA emerges from within pol II at ~17 nt [54,55] . Complexes paused over about the next 15 bases have a strong tendency to backtrack. The exact location of the onset of backtracking, and the extent to which particular complexes backtrack, is a function of promoter sequence, but all backtracked complexes apparently retreat to a common template location, essentially the same as that in stage E [57]. Downstream of ~+23, there is no measurable tendency for complexes to slip during transcription of repeated template segments [34]. (G) Clearance is apparently complete at this point, with no general tendency to backtrack.