The conserved SEN1 DNA/RNA helicase has multiple functions during yeast meiosis
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, the highly conserved, topisomerase-like protein, Spo11, generates ~200 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. One way of removing DNA/RNA hybrids is degradation of the RNA by RNase H. Phenotypic characterization of organisms lacking RNase H activity has demonstrated that regulation of the level of DNA-RNA hybrids is important for meiotic double strand break repair. Sen1 is an essential 5'-3' DNA-RNA helicase that can remove DNA-RNA hybrids by unwinding the RNA. Sen1 is orthologous to the mammalian Senataxin (SETX) helicase. 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 SETX's 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 functions that promote yeast meiosis. First, it enables the timely expression of IME1-regulated early genes. Second, it helps prevent/remove DNA-RNA hybrids that form during premeiotic S phase. Third, it facilitates repair of Spo11 double strand breaks generated during Prophase I, as well as chromosome synapsis. Overall design: RNA was extacted from SEN1 and sen1-md yeast (Saccharomyces cerevisiae) cells using the Qiagen RNeasy kit  at different times after the onset of meiosis.  Sequencing libraries were generated from enriched PolyA RNA using NEBNext Ultra RNA Library kit and analyzed by Illumina paired end sequencing.