Supplemental Material for Zhou et al., 2020

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Amino acid substitutions are commonly found in human transcription factors, yet the functional consequence of much of this variation remains unknown, even in wellcharacterized DNA-binding domains. Here, we examine how six single amino acid variants in the DNA-binding domain of Ste12 – a yeast transcription factor regulating mating and invasion – alter Ste12 genome binding, motif recognition and gene expression to yield markedly different phenotypes. Using a combination of the calling card method, RNA sequencing and SELEX, we find that variants with dissimilar binding and expression profiles can converge onto similar cellular behaviors. Mating-defective variants led to decreased expression of distinct subsets of genes necessary for mating. Hyper-invasive variants also decreased expression of subsets of genes involved in mating, but increased the expression of other subsets of genes associated with the cellular response to osmotic stress. While single amino acid changes in the coding region of this transcription factor result in complex regulatory reconfiguration, the major phenotypic consequences for the cell appear to depend on changes in the expression of a small number of genes with related functions.