Natural Genetic And Epigenetic Variation At Retroposon Loci In Arabidopsis

Abstract

In both plants and animals, transposable elements are epigenetically regulated to maintain genomic integrity. DNA methylation (5-methylcytosine) is an important epigenetic modification that maintains transcriptional silencing at repetitive sequences and transposons. Here, I use the Sadhu family of non-LTR retroposons in Arabidopsis thaliana as models to understand the connection between genetic and epigenetic variation. There are only 16 full-length Sadhu elements in the Arabidopsis thaliana genome, and these elements are genetically diverged, sharing only 75% sequence identity. We analyzed both genetic and epigenetic variation in two different Sadhu elements, the heterochromatic Sadhu1-1 and the euchromatic Sadhu6-1. For both of these elements, we determined that Sadhu is not uniformly controlled but can exist in an epigenetically active or a repressed state. To test the source of variation in epigenetic state at these loci, we crossed two strains with differentially methylated Sadhu elements and observed no trans-activation of the silenced allele, nor repression of the transcribed element in the hybrids. Our results suggest that Sadhu elements are inherited as pure epialleles that differ between strains. Additionally, I investigated intrastrain stability of Sadhu transcription. I used a ddm1 mutation to genetically activate a silenced Sadhu1-1 epiallele. After restoring DDM1, we monitored transcription in these plants for eight meiotic generations and determined that transcription remains on, but is variable in these lines. My findings indicate that maintenance of DNA methylation is sufficient to silence Sadhu elements; however, a loss of methylation does not trigger de novo methylation and epigenetic silencing is not efficiently repaired. The variation within the Sadhu family provides new insights into the stability of DNA methylation at transposons and can serve as a model for natural epigenetic variation.