Accumulation ofcis- andtrans-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species

Abstract

Gene regulatory variations accumulate during evolution and alter gene expression. While the importance of expression variation in phenotypic evolution is well established, the molecular basis remains largely unknown. Here, we examine two closely related yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus, that show phenotypical differences in morphology and cell cycle progression when grown in the same environment. By profiling the cell cycle transcriptome and binding of key transcription factors (TFs) in the two species and their hybrid, we show that changes in expression levels and dynamics of oscillating genes is dominated by upstream trans-variations. We find that multiple cell cycle regulators show both cis- and trans- regulatory variations, which alters their expression in favor of the different cell cycle phenotypes. Moreover, we show that variations in the cell cycle TFs, Fkh1 and Fkh2, affects both the expression of target genes, and the binding specificity of an interacting TF, Ace2. Our study reveals how multiple variations accumulate and propagate through the gene regulatory network, alter TFs binding, contributing to phenotypic changes in cell cycle progression.

Evolution of binding preferences among whole-genome duplicated transcription factors

“…Colonies were confirmed using PCR and gel electrophoresis followed by DNA sequencing. Few strains were generated and profiled in previous studies from the lab ( Brodsky et al, 2020 ; Lupo et al, 2021 ).…”

Evolution of transcription factor binding through sequence variations and turnover of binding sites

“…We found this method to give a highly reproducible and spatially resolved TF binding maps ( Bar-Ziv et al 2020 ; Brodsky et al 2020 ; Gera et al 2021 ; Lupo et al 2021 ). We previously observed that orthologous TF proteins bind to similar locations in the hybrid genome, and at a similar level, by profiling both the S. cerevisiae TF ortholog and the S. paradoxus ortholog in separate experiments ( Lupo et al 2021 ). This observation was consistent with the generally slow evolution of TF preferences ( Carroll 2005 ).…”

“…Both species’ genomes are highly compact with short intergenic regions (200–400 bp) that function primarily as gene promoters. We and others have previously used this hybrid as a model for studying the principles of regulatory evolution ( Tirosh et al 2009 ; Emerson et al 2010 ; Artieri and Fraser 2014 ; Metzger et al 2016 ; Weiss et al 2018 ; Krieger et al 2020 ; Lupo et al 2021 ).…”

“…For ChEC-seq, transcription factors were tagged with MNase on their C terminus, by amplifying the MNase-KanMX cassette from the pGZ108 plasmid, a gift from Steven Henikoff. Strains that were previously generated in our laboratory were based on transformation of BY4741 with MNase-KanMX cassette, with an ORF-MNase linker of 33 amino acids ( Bar-Ziv et al 2020 ; Brodsky et al 2020 ; Lupo et al 2021 ). In this study, strains were generated on the background of the C-SWAT library ( Meurer et al 2018 ) a gift from Maya Schuldiner.…”

“…The hybrid's nucleus contains two related parental genomes. By applying allele-specific mapping, we could directly compare TF binding to the two genomes while ensuring a uniform trans -regulatory environment ( Tirosh et al 2009 ; Emerson et al 2010 ; Metzger et al 2016 ; Wong et al 2017 ; Krieger et al 2020 ; Floc'hlay et al 2021 ; Hill et al 2021 ; Lupo et al 2021 ; Yang et al 2021 ). Our analysis examined the contribution of two types of variations, in sequence motifs and in chromatin accessibility, to divergence of TF binding at individual binding sites.…”