Mating-type switching by homology-directed recombinational repair: a matter of choice

Abstract

In eukaryotes, all DNA transactions happen in the context of chromatin that often takes part in regulatory mechanisms. In particular, chromatin structure can regulate exchanges of DNA occurring through homologous recombination. Few systems have provided as detailed a view on this phenomenon as mating-type switching in yeast. Mating-type switching entails the choice of a template for the gene conversions of the expressed mating-type locus. In the fission yeast Schizosaccharomyces pombe, correct template choice requires two competing small recombination enhancers, SRE2 and SRE3, that function in the context of heterochromatin. These two enhancers act with the Swi2/Swi5 recombination accessory complex to initiate strand exchange in a cell-type-specific manner, from SRE2 in M cells and SRE3 in P cells. New research indicates that the Set1C complex, responsible for H3K4 methylation, and the Brl2 ubiquitin ligase, that catalyzes H2BK119 ubiquitylation, participate in the cell-type-specific selection of SRE2 or SRE3. Here, we review these findings, compare donor preference in S. pombe to the distantly related budding yeast Saccharomyces cerevisiae, and contrast the positive effects of heterochromatin on the donor selection process with other situations, where heterochromatin represses recombination.

Keywords: Chromatin structure; Gene conversion; Histone modifications; Homology-directed repair; Mating-type switching; Recombination.

Fig. 1

Mating-type cassettes and mating-type switching patterns in S. pombe (a) and S. cerevisiae (b). In S. pombe, the expressed mat1 locus switches between mat1-P and mat1-M due to gene conversions by the linked mat2-P and mat3-M silent loci. In S. cerevisiae, the expressed MAT locus switches between MATα and MATa due to conversions by HMLα and HMRa. Silent heterochromatic regions are indicated by thick black lines. Gene conversions are initiated in both cases by a DNA break at the expressed locus followed by strand invasion at one of the silent cassettes. Strand invasion occurs at homology boxes present at the three cassettes: H1 in S. pombe and Z1 in S. cerevisiae. In S. pombe, the DNA break is formed during DNA replication in cells that have acquired an imprint during the previous DNA replication (switchable cells), and only one of the newly synthesized chromatids undergoes conversion producing one switched and one unswitched progeny (examples framed in red in cell pedigree). In S. cerevisiae, the DNA break is formed and used in the G1 phase of the cell cycle, exclusively in mother cells due to restricted expression of the HO endonuclease in mother cells, this produces pairs of switched cells after DNA replication and cell division (examples framed in red). The silent cassettes that contain mating-type information opposite to the expressed cell type are preferentially chosen in both yeasts, giving rise to the observed high efficiency of switching in the progeny of switching-competent cells; however, donor preference is not determined by the mating-type-specific sequences in the donors

Fig. 2

Heterochromatin at the donor loci. a In S. pombe, histone deacetylation by several HDACs (SHREC, Clr6, Sir2) together with histone H3K9 methylation by CLRC forms heterochromatin over a 20 kb domain between the IR-L and IR-R boundaries. Following histone modification, the chromodomain protein Swi6 associates with the entire 20 kb region. cenH is an RNA-interference heterochromatin nucleation center with centromere homology. b In S. cerevisiae, heterochromatin results from histone deacetylation and association of Sir proteins in two smaller domains, each < 3 kb, at the HML and HMR loci. At each cassette, the E and I silencers recruit various combinations of DNA-binding proteins, ORC, Rap1, and Abf1, to initiate heterochromatin formation

Fig. 3

Choice of recombination enhancers in S. pombe and S. cerevisiae. aSchizosaccharomyces pombe SRE2 and SRE3 enhancers. In P cells, the Swi2/Swi5 complex is exclusively associated with the recombination enhancer SRE3; this facilitates Rad51-mediated strand invasion at the H1 region of mat3 and thus promotes switching from mat1-P to mat1-M. In M cells, the Swi2/Swi5 complex is more broadly associated with the entire heterochromatic domain, this association requires the chromodomain protein Swi6. Under these conditions, the SRE2 enhancer is preferred over SRE3 leading to switching from mat1-M to mat1-P. The use of SRE3 in M cells might be limited by Set1C. bSaccharomyces cerevisiae RE enhancer. In MATa cells, RE, bound by multiple copies of the Fkh1 protein, establishes a physical contact with the MAT locus through the interaction of Fkh1’s phospho-threonine binding domain with phosphorylated proteins located at or near the DSB; these proteins include Mph1 and Fdo1. RE binding at the site of the DSB shortens the distance between MATa and HMLα, favoring Rad51-mediated recombination between MAT and HMLα. In MATα cells, binding of Fkh1 to RE is disrupted by the repressor, Mcm1/Matα2; consequently, HMRa, closer to MAT, is then preferred