Discrimination between Paralogs using Microarray Analysis: Application to the Yap1p and Yap2p Transcriptional Networks

Abstract

Ohno [Ohno, S. (1970) in Evolution by Gene Duplication, Springer, New York] proposed that gene duplication with subsequent divergence of paralogs could be a major force in the evolution of new gene functions. In practice the functional differences between closely related homologues produced by duplications can be subtle and difficult to separate experimentally. Here we show that DNA microarrays can distinguish the functions of two closely related homologues from the yeast Saccharomyces cerevisiae, Yap1p and Yap2p. Although Yap1p and Yap2p are both bZIP transcription factors involved in multiple stress responses and are 88% identical in their DNA binding domains, our work shows that these proteins activate nonoverlapping sets of genes. Yap1p controls a set of genes involved in detoxifying the effects of reactive oxygen species, whereas Yap2p controls a set of genes over represented for the function of stabilizing proteins. In addition we show that the binding sites in the promoters of the Yap1p-dependent genes differ from the sites in the promoters of Yap2p-dependent genes and we validate experimentally that these differences are important for regulation by Yap1p. We conclude that while Yap1p and Yap2p may have some overlapping functions they are clearly not redundant and, more generally, that DNA microarray analysis will be an important tool for distinguishing the functions of the large numbers of highly conserved genes found in all eukaryotic genomes.

A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response

“…(As a baseline comparison, the average overlap between the Yaps and an unrelated TF, Pdr1, was 2.9% under nominal conditions.) This result confirmed and expanded previous observations that Yaps have partially overlapping but nonredundant functions (5,6,19).…”

“…Studies suggest that Yaps 2 and 6 can function either as activators or repressors, depending on the regulated genes (6,29,30). To further explore this phenomenon and its underlying mechanisms, we applied network component analysis (NCA) (31) to infer the regulatory directions (activating, repressing) of each Yap on its target genes.…”

“…The Yap family belongs to the bZIP superfamily of TFs that is widely conserved from yeast to human. Specificity of gene regulation among paralogous Yaps has been attributed to two mechanisms: (i) slight but important differences in the DNA binding motifs targeted by different Yap TFs, as in the case of Yap1 versus Yap2 (6), and (ii) Variation in the regulatory domains present within each Yap protein that are modulated by specific upstream activation signals, i.e., Yap1 is modulated by intramolecular disulfide bond formation (7) and Yap4 is modulated by protein phosphorylation (8). A variety of other mechanisms for achieving specificity are also likely, although they have not yet been systematically demonstrated for the Yap proteins.…”

Aft1p and Aft2p Mediate Iron-responsive Gene Expression in Yeast through Related Promoter Elements

“…Analysis of global gene expression using microarrays has shown that although Yap1p and Yap2p are both involved in the response to cellular stresses, they regulate different regulons (7). The mechanism(s) of Yap1p/Yap2p gene selectivity are not understood but may include variations in the base pairs flanking the consensus Yap binding site (7).…”

The S. cerevisiae Yap1 and Yap2 transcription factors share a common cadmium‐sensing domain

“…Other putative targets of Yap2 that encode activities involved in protein folding have been suggested by microarray analyses, but these have not yet been validated [37]. It has also Cd C356 C391 Yap2 Fig.…”