Genetic and molecular analysis of chromosomal determinants of transposon silencing in euchromatin

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Eukaryotic genomes contain a large proportion of transposable elements (TE) and repetitive sequences. Through their mobilization and transposition, these sequences have a high mutagenic potential. This threatens genome integrity but also provides an important source of genetic variation for selection to act upon. Thus, organisms have evolved mechanisms to limit TE activity. Much progress towards an understanding of mechanisms underlying TE silencing has been made. However, many aspects of TE interaction with the host chromatin remain unresolved. In particular, it remains unknown how genes limit/affect the silencing of nearby TE. We have previously found that TE inserted into the 3(prime) end of protein-coding genes escape silencing and that there is considerable variation in the silencing of individual TEs in the A. thaliana lineage. These insertions are stable at the evolutionary scale and do not interfere with transcription of the TE or the protein gene. Based on these findings, we will focus on two key questions: 1) How widespread is the correlation between insertion into the 3(prime) end of genes and escape from silencing? 2) What is the mechanistic basis of this escape from silencing? To investigate these questions, we will bioinformatically analyze how widespread the correlation between 3(prime) end insertion and loss of silencing is at the population level. We will further investigate the mechanistic basis of this escape from silencing by testing the involvement of nucleosome remodeling, 3(prime) end processing and anti-silencing factors. One such anti-silencing factor has been previously identified by the applicants. We will correlate this with the behavior of newly generated TE insertions generated in the lab. Together, this work will provide insights into the important question of how transposon silencing is initiated and maintained in a euchromatic context, as well as how TE and host genes reciprocally influence each other. In addition, this work will provide insight into the regulation of 3(prime) end formation and termination of transcription. Thus, this study will contribute to our understanding of genome organization and regulation.