Discovery and Properties of Small RNAs from Meiotic Silencing by Unpaired DNA in Neurospora crassa
Genome defense likely evolved to prevent the spread of transposable elements and invading viruses. Effective genome defense mechanisms have limited colonization of the Neurospora crassa genome by transposable elements. A novel DNA transposon named Sly1-1 was discovered in the genome of the most widely used lab "wildtype" strain FGSC 2489 (OR74A). Meiotic silencing by unpaired DNA (MSUD), also simply called "meiotic silencing", prevents the expression of regions of the genome that are unpaired during karyogamy. This mechanism is posttranscriptional and involves the production of small RNA, so called "masiRNAs" by proteins homologous to those involved in RNAi silencing pathways in animals, fungi and plants. Here, I demonstrate production of small RNAs when Sly1-1 was unpaired in a cross between two wild type strains. These small RNAs are dependent on SAD-1, an RNA-dependent RNA polymerase necessary for meiotic silencing. I present the first case of endogenously produced masiRNA from a novel N. crassa DNA transposable element during the sexual development. By comparing genome sequences of two mating partners, I also identified (1) unpaired regions undergoing meiotic silencing, some of which contained the repetitive sequences and transposon relics. Small RNA produced from such regions shared the same features as masiRNAs; (2) unpaired regions immune to meiotic silencing with genes contained protected from meiotic silencing via abolishing small RNA production; (3) common regions shared by two mating patterns but with small RNAs production during karyogamy. The dissection of these regions revealed the role of meiotic silencing on resisting repetitive sequences and on compromising the unpaired genes essential in sexual development.