The Dual Impact of Active and Silenced Transposons on Meiotic Recombination - PROJECT SUMMARY Meiotic recombination is a fundamental process in sexually reproducing eukaryotic organisms that generates genetic diversity and ensures the accurate segregation of homologous chromosomes. Disruptions in this process can lead to severe consequences, including infertility and genetic disorders. Meiotic recombination is intricately regulated by both genetic and epigenetic factors. There is growing evidence that transposable elements (TEs), which are primary targets of epigenetic silencing in both plants and mammals, can influence recombination both genetically, through the induction of double-strand breaks (DSBs), and epigenetically, by introducing new methylated and histone-modified sequences near genes. The long-term goal of our lab is to identify and manipulate genetic and epigenetic factors that influence meiotic recombination. The overall objective of this proposal is to address critical knowledge gaps in understanding how active and silenced TEs shape recombination, using maize and rice as models because of their abundance of naturally active TEs. Based on our preliminary data, our central hypothesis is that both active and silenced transposons remodel recombination landscapes by affecting crossover interference, the synaptonemal complex, DSB repair, and chromatin structure. To test this hypothesis, we will first investigate how active Mutator (Mu) transposons in maize, which induce abundant DSBs during sporophytic germline development and in gametophytes, affect recombination. We will generate high-resolution crossover maps, perform a genome-wide assessment of recombination frequency in the vicinity of Mu insertions, and determine whether Mu-derived DSBs can introduce crossovers. We will also examine whether Mu excision or insertion alters chromatin structure, chromatin accessibility, and 3D genome organization at insertion sites and their flanking regions. Second, we will study the impact of miniature inverted repeat elements (MITEs) on recombination in rice using recombinant inbred line populations with high versus low MITE copy numbers. Finally, we will examine how silenced TEs near active genes influence recombination using the mop1 (mediator of paramutation 1) mutant, which largely removes CHH methylation near genes and redistributes recombination landscapes. We will investigate how DNA methylation at TEs affects DSB formation, crossover interference, chromosome axis organization, synaptonemal complex dynamics, and chromatin structure in a sex-specific manner. This study will contribute to a comprehensive understanding of how TEs, DNA methylation, and chromatin structure interact to shape meiotic recombination landscapes in maize and rice, with broad implications for other eukaryotes.
