Mechanism of facilitated homology search and the logic of its meiotic regulations

DNA double-strand breaks (DSB) repair by homologous recombination (HR) entails identification of an intact homologous template DNA molecule in the genome. Homology search is guided by the DSB-flanking ssDNA sequence assembled into a RecA-family nucleoprotein filament (NPF).

A biased version of this process, regulated in an ill-defined manner by chromosomes structure and meiosis-specific HR proteins, also underlies homolog recognition and recombination during meiosis I in most examined eukaryotes.

Despite its centrality for genome maintenance and sexual reproduction, how homology search operates in cells and the nature of its meiotic regulations are largely unknown.

Our goal is to solve these two major biological conundrums with a simple idea: that substrate properties (chromatin composition and motion) provide cues for search simplification and regulation.First, we will address the existence of a homology search facilitation mechanism based on combined (i) DNA occlusion by nucleosome and (ii) seeding of homology search by pioneer transcription factors (WP1).

These insights will be applied to accelerate yeast evolution and improve gene-editing.

Second, we will address how uncoordinated movements of semi-rigid meiotic chromosomes can generate mechanical cues underlying HR regulations that result in patterned recombination between homologs (WP2).

The experimental strategy will involve extensive genetic engineering and large synthetic chromosomal regions for targeted alteration of chromatin composition, chromosome physical properties and chromosome motion in cis.

Novel genomic and molecular approaches we developed to directly detect transient HR intermediates in yeast make this project uniquely feasible.

This work should elucidate enigmatic interplays between chromosome biology and conserved DNA metabolic processes in mitosis and meiosis, broadens the current paradigm of facilitated target search by proteins in DNA, and yield tools of broad biotechnological interest.