In most eukaryotes, including the majority of fungi, expression of sterol 
biosynthesis genes is regulated by Sterol-Regulatory Element Binding Proteins 
(SREBPs), which are basic helix-loop-helix transcription activators. However, in 
yeasts such as Saccharomyces cerevisiae and Candida albicans sterol synthesis is 
instead regulated by Upc2, an unrelated transcription factor with a Gal4-type 
zinc finger. The SREBPs in S. cerevisiae (Hms1) and C. albicans (Cph2) have lost 
a domain, are not major regulators of sterol synthesis, and instead regulate 
filamentous growth. We report here that rewiring of the sterol regulon, with 
Upc2 taking over from SREBP, likely occurred in the common ancestor of all 
Saccharomycotina. Yarrowia lipolytica, a deep-branching species, is the only 
genome known to contain intact and full-length orthologs of both SREBP (Sre1) 
and Upc2. Deleting YlUPC2, but not YlSRE1, confers susceptibility to azole 
drugs. Sterol levels are significantly reduced in the YlUPC2 deletion. RNA-seq 
analysis shows that hypoxic regulation of sterol synthesis genes in Y. 
lipolytica is predominantly mediated by Upc2. However, YlSre1 still retains a 
role in hypoxic regulation; growth of Y. lipolytica in hypoxic conditions is 
reduced in a Ylupc2 deletion and is abolished in a Ylsre1/Ylupc2 double 
deletion, and YlSre1 regulates sterol gene expression during hypoxia adaptation. 
We show that YlSRE1, and to a lesser extent YlUPC2, are required for switching 
from yeast to filamentous growth in hypoxia. Sre1 appears to have an ancestral 
role in the regulation of filamentation, which became decoupled from its role in 
sterol gene regulation by the arrival of Upc2 in the Saccharomycotina.