Yeast Lachancea Kluyveri uses tripartite mechanism for haploid specific gene repression [ChIP-seq]

Over evolutionary timescales, the logic and pattern of cell-type specific gene expression can remain constant, yet the molecular mechanisms underlying such regulation can drift between alternative forms. Here, we document a new, especially clear example of this principle in the regulation of the haploid-specific genes across a wide group of fungal species. For most species, transcription of these genes is repressed in the a/ a cell type by a heterodimer of two homeodomain proteins, Mata1 and Mata2. We show that in the species Lachancea kluveri, repression of one haploid-specific gene (GPA1) requires, in addition to Mata1 and Mata2, a third regulatory protein, Mcm1. Model building, based on x-ray crystal structures of the three proteins, rationalizes the requirement for all three proteins: no single pair of the proteins is optimally arranged and we show that no single pair can bring about repression. Although the three-part solution is used to regulate GPA1 in L. kluveri, the other haploid specific genes in this species are regulated by the more conventional two-protein mechanism. This case study exemplifies the idea that the energy of DNA binding can be “shared out” in different ways and can result is different DNA-binding solutions across different genes—while maintaining the same pattern of gene expression. Overall design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) of tagged Matalpha2 to assay Mata1 dependent Matalpha2 binding in a/alpha cell in the yeast Lachancea Kluyveri. To assay binding, ChIP-seq from tagged a/alpha cells was compared to untagged a/alpha cells and input. The same was done for alpha cells. Then results from alpha cell ChIP-seq were used as a control for Matalpha2 binding events that occur in both a/alpha and alpha cells, allowing us to find a/alpha cell specific binding of Matalpha2.