Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program
Fig 1
A new resource allocation model partitions the genome in five expression sectors.
A) Top. Resource allocation model (Model 1) based on three sectors in which the expression of their constituent genes increases (positive genes, blue), decreases (negative genes, red), or remains constant (invariant genes, brown) with increasing growth rate. Bottom. Resource allocation model (Model 2) based on a specific and nonspecific sectors in which the expression of their constituent genes increases (nonspecific, white) or decreases (specific, grey) with increasing growth rate. B) Partition of genome expression into five sectors that combine the two previous models. A model-1-like partition appears as a fine structure within the nonspecific sector. We labelled this scheme as Model 3. C) Fractional promoter activity (fPA) for a transition between two example conditions increasing growth (glycerol to glucose). Promoters can be classified into the five sectors of model 3 depending on how their fPA changes (yellow dots indicate those with very low activity in both conditions). Repressed and activated promoters constitute the specific sector. Nonspecific promoters are constituted by one invariant type and two other subclasses whose fPA depends on the growing condition.