Novel metrics for promoter activity profiles

Novel metrics for promoter activity profiles

Colin Semple, James Prendergast

The relative amount of transcriptional "noise" versus functional transcription has been the subject of much debate in recent years. Even relatively rare, low abundance transcripts have been shown to have direct, functional roles in gene regulation, while others mirror the dynamics of chromatin composition at promoters. A diverse population of long and short RNAs transcribed at promoters can mediate regulatory events based upon chromatin remodelling (Beisel and Paro, 2011), and it seems that populations of very short transcripts may reflect the transit or pausing of RNA Pol II across promoters (Taft et al, 2009). It follows that the profiles of transcriptional activity across a collection of TSSs, if studied at sufficient depth, should differentiate promoters subject to different constellations of regulatory events.

We have developed a novel metric to calculate promoter activity profiles across libraries using FANTOM5 CAGE data, and have shown that such profiles are complementary to the study of traditional expression patterns, revealing novel insights into regulation. We intend to estimate the degree of "noise" present in activity profiles and their divergence across evolutionary time.