The conserved SEN1 DNA/RNA helicase has multiple functions during yeast meiosis

Abstract

Diploid Saccharomyces cerevisiae cells undergo meiosis when they are starved of nitrogen in the presence of a non-fermentable carbon source. Nutrient starvation triggers expression of Ime1, a master regulatory protein required to activate transcription of meiotic "early genes" that mediate premeiotic S phase and prophase I processes, including recombination and chromosome synapsis. During prophase I, the highly conserved, toposomerase-like protein, Spo11, creates double strand breaks that are used to identify homologous chromosomes and generate crossovers between them. DNA:RNA hybrids are formed when an RNA molecule anneals to a complementary strand of DNA and are present at the ends of double strand breaks during prophase I of meiosis in a variety of organisms. DNA:RNA hybrids can be removed by degradation of the RNA by RNase H or by unwinding of the RNA by an essential, multi-functional DNA:RNA helicase called Sen1. Sen1 is orthologous to the mammalian Senataxin (SETX) helicase. Phenotypic characterization of mouse mutants lacking either Senataxin or RNase H activity exhibit male infertility and defects in double strand break repair. SETX is also required for meiotic sex chromosome inactivation, making it unclear whether SETXs role in meiotic recombination is direct or an indirect consequence due to defects in SETX functions that affect transcription. Using a variety of orthogonal approaches, this work demonstrates that SEN1 has multiple, temporally distinct roles that promote yeast meiosis. First, it enables the timely expression of IME1-regulated early genes. Second, it helps prevent and/or remove DNA:RNA hybrids that form during premeiotic S phase. Third, it facilitates both repair of Spo11 generated double strand breaks generated during prophase I and chromosome synapsis. AUTHOR SUMMARYDNA:RNA hybrids are unusual structures found throughout the genomes of many species, including yeast and mammals. While DNA:RNA hybrids may promote various cellular functions, persistent hybrids lead to double strand breaks, resulting in genomic instability. DNA:RNA hybrid formation and removal are therefore highly regulated by enzymes that either degrade or unwind RNA from the hybrid. Meiosis is the specialized cell division that creates haploid gametes for sexual reproduction. Previous work in yeast and mammals showed that elimination of DNA:RNA hybrids by RNase H facilitates meiotic recombination. This work demonstrates that the conserved Sen1 DNA:RNA helicase regulates the presence of DNA:RNA hybrids in three temporally distinct processes during yeast meiosis. First, SEN1 allows for meiosis-specific genes to be expressed at the proper time to allow entry into meiosis. Second, SEN1 prevents the accumulation of hybrids during premeiotic DNA replication. Third, SEN1 promotes the repair of programmed meiotic double strand breaks that are necessary to form crossovers between homologous chromosomes to allow their proper segregation at the first meiotic division. Given the evolutionary conservation of Sen1 with its mammalian counterpart, Senataxin, studies of Sen1 function in yeast are likely to be informative about the regulation of DNA:RNA hybrids during humans as well.