TY - JOUR T1 - Recombination-independent recognition of DNA homology for meiotic silencing in <em>Neurospora crassa</em> JF - bioRxiv DO - 10.1101/573907 SP - 573907 AU - Nicholas Rhoades AU - Germano Cecere AU - Thomas Hammond AU - Eugene Gladyshev Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/03/11/573907.abstract N2 - Pairing of homologous chromosomes represents a key aspect of meiosis in nearly all sexually reproducing species. While meiotic pairing requires the formation of double-strand DNA breaks in some organisms, in many others it can proceed in the apparent absence of DNA breakage and recombination. The mechanistic nature of such recombination-independent pairing represents a fundamental question in molecular biology. Using “meiotic silencing by unpaired DNA” (MSUD) in the fungus Neurospora crassa as a model system, we demonstrate the existence of a cardinally new solution to the problem of inter-chromosomal homology recognition during meiosis. Here we take advantage of the unique ability of MSUD to efficiently detect and silence (by RNA interference) any relatively short DNA fragment lacking a homologous allelic partner. We show that MSUD does not require the function of eukaryotic RecA proteins and the type II topoisomerase-like protein Spo11. We further show that MSUD can recognize patterns of weak interspersed homology in which short units of sequence identity are arrayed with a periodicity of 11 base-pairs (bp). Taken together, these results reveal the function of a recombination-independent homology-directed process in guiding the expression of small interfering RNAs and suggest that meiotic chromosomes can be evaluated for sequence homology at base-pair resolution by a mechanism that operates on intact DNA molecules. ER -