Transcription Initiation: Can It Get Any More Complex?

Source: Revyakin et al. (2006). Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching. Science 314:1139-1143.

Transcription initiation involves a number of steps:

1. Attachment to the

 promoter (clodes complex: RPc).

2. Unwinding the DNA ~1 turn to form the open complex (RPo).

3. Synthesis and release of short RNAs (RPitc).

4. Promoter escape and elongation.

The most complex is RPitc in which short RNA transcription is ocurring (~8-11 nt); however, RNA polymerase is not moving as determined by footprinting assays. There have been three models for explaining this behavior:

1. Scrunching: DNA is contracted inward.

2. inchworming: RNA pol is conformationally expanded.

3. transient excursions: RNA pol moves back and forth with long intervals.

If the first model is true, at RPitc stage the DNA is being unwound. The authors have made an experimental setup for detecting these variations (see below) and they use this system to show that this model is correct.