Its out on the Molecular Systems Biology website. Yay!
This paper summarizes quite a bit of work by Naomi and Ilan. It started with "here is a short 2-week project" and ended as big part of Naomi's PHD and a massive paper.
Highlights (from our synopsis):
By tracing the evolutionary history of transcriptional networks across 23 fungi, two seemingly contradictory trends are observed: rapid target turnover and conserved function. This is reconciled by a model that invokes strong selection to conserve the overall function of a motif, but not its individual targets.
- The vast majority of cis-regulatory elements in genes’ promoters are rapidly gained and lost across species.
- Despite this rapid turnover, most transcription factors are associated with a conserved function even at great evolutionary distances.
- A functional selection turnover model reconciles these two phenomena by invoking a preference to conserve the overall function of the motif but not the individual target genes.
- Our model fits the variation in measured transcription factor binding profiles across species in both yeasts and mammals.