Understanding regulation of meiosis in Arabidopsis and maize

Supplemental file(s) description: Chapter 2 Supplementary Tables, Chapter 3 Supplementary TablesMeiosis is a specialized cell division that is required for sexual reproduction. Homologous chromosome pairing and meiotic recombination are two defining processes of prophase I of meiosis and are required for the generation of genetic variation. Core proteins involved in these processes are well studied, but it is not well understood how meiosis is regulated. In this dissertation, I shed light on how meiosis is regulated by long non-coding RNAs (lncRNAs) in Arabidopsis thaliana, as well as how meiotic recombination is regulated by chromatin in maize. Many long non-coding RNAs (lncRNAs) have been identified in various species but few have been functionally analyzed. Of the few lncRNAs that have been analyzed, they have been found to play roles in regulating gene expression and modifying chromatin. However, the functions of the vast majority of them are unknown and no lncRNAs have been identified in Arabidopsis meiosis. On the other hand, significantly more genes are expressed during meiosis than the number of genes actually required for meiosis completion, suggesting that there is a mechanism controlling gene expression post-transcriptionally, possibly involving lncRNAs. This situation prompted us to conduct a systematic analysis of lncRNAs in Arabidopsis meiosis. We generated a bioinformatics pipeline that utilizes RNA-seq data from Arabidopsis meiocytes and somatic tissues to identify novel lncRNAs that are specific to meiosis. We then established a multistep mutant screen to identify lncRNAs that are functional in meiosis and found that lncRNAs play a role in overall fertility in Arabidopsis thaliana. Chapter 3 of this dissertation focuses on understanding the role of chromatin in the regulation of meiotic recombination events that result in crossovers (COs) in maize. In this species, double strand breaks (DSBs) are evenly distributed along chromosomes, including pericentromeric and centromeric regions. However, CO distribution does not follow the DSB distribution. Instead, COs are enriched in distal chromosome regions and suppressed in pericentromeric and centromeric regions. We investigated the dynamics of recombination events in relationship to chromatin states in order to understand how this distribution is formed. We further studied the CO/non-crossover (NCO) decision through its relationship with chromatin. We found that DNA methylation is a major contributor to the decision of which DSBs become COs and this decision is progressively enforced when meiotic DSBs are repaired. Interestingly, this process proceeds differently in B73 and CML228, two maize inbreds with dramatically differing numbers of recombination events