We have invested in the elucidation of the molecular basis of the Pch2/ORC system as an “anti-DSB” system. We have established a global map of Pch2-chromatin association, with a focus on rDNA association. In Aim 2.1. we have used ChIP-seq to map the binding patterns of Pch2 along the rDNA chromatin and the entire genome, as proposed. This data has been used to show that 1) rDNA binding is dependent on ORC, and 2) rDNA binding is related to PolI-driven rRNA transcription. Likewise, the euchromatin binding patterns have been mapped, and show dependencies on ORC and PolII-driven transcription. A paper describing these finding was published (
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008905). In Aim 2.2. and 2.3. we determined that Pch2 interacts with the other ORC subunits (Orc2 and 5, specifically), confirming our hypothesis that the entire ORC complex interacts with Pch2. Using in vitro reconstitution, we created a Pch2-ORC hexamer-hexamer assembly, and we have used in vitro analysis to delineate the binding interfaces of this assembly. Surprisingly, we have found that Orc1 is a crucial interactor of Pch2, and that this interaction represents a non-canonical association of ORC to Pch2. This work was also published during this period (
https://www.life-science-alliance.org/content/3/11/e201900630). We have slightly deviated from the work plan, as under Aim 2.2 we have already generated an analysis of the Pch2 interactome, using MS-analysis; this analysis was planned to be executed in Aim 2.5. Informed by the MS analysis, we have focused our attention in the interaction between Pch2 and Msh4/5, an important meiotic ATPase that we have found to interact with Pch2). Under Aim 2.4. we studied genetic and functional interaction between Pch2, Hop1 and Zip1, which is able to explain many of the roles that are ascribed to Pch2 in meiotic G2/prophase both at the rDNA and euchromatin. This work has yielded important insights into the wiring of the meiotic checkpoint and the role of Pch2 therein. This work was also published in this reporting period (
https://www.cell.com/current-biology/fulltext/S0960-9822(20)31254-9).
We have developed a novel technology for ectopic targeting of selected proteins to defined regions. We have opted for a CRISPR/Cas-based targeting system. This system utilizes a nuclease-dead version of Cas9, that can be fused to proteins of interest to target these fusion proteins to genomic regions of choice. We have adapted this system to be used in meiosis, by generating dCas9-contructs that are meiosis-specifically expressed. These systems are combined with specific small guide RNAs (sgRNAs) of choice. We have shown that this system can successfully be used to target proteins of choice to defined regions within the genome. We have so far combined this system with a recently developed fluorescent-based recombination reporter that can reliably measure crossover frequencies within regions of choice. The advantage of this reporter is that is allows the use of microscopy-based analysis instead of the labour-intensive classical analysis of crossover frequencies via yeast tetrad dissection. In another project, my laboratory has shown that this approach (of combining dCas9-based targeting with the fluorescent reporter) can successfully be used to dissect control of local crossover recombination. For Aim 1.1 and 1.2. we have established a new system to interrogate DNA break and recombinational control, based on CRISPR/dCas9. These systems have been shown to be able to locally influence recombination patterns, and we have used this to delineate local DSB suppression. These findings were published recently (
https://www.genetics.org/content/216/2/395.long).