Research

The main theme of my research at UCI has been the study of transposable elements (TEs) and the consequences of their activity in the genomes of plants. TEs are famous for their sometimes dramatic deleterious effects, but can they also contribute in a more positive manner to their host’s genome? The answer is an emphatic “yes”: TEs contribute to protein coding sequence and are able to alter the expression of genes, making them key players in the evolution of genomes. Since the sole function of a TE is to copy itself, TEs are surprisingly rare in genomes. What are the forces keeping TEs from overwhelming genomes? I am interested in how the forces of recombination and selection keep TEs under control.

I have discovered numerous genes in Arabidopsis thaliana where TE sequence is present in the protein coding sequence. Using stringent BLAST searches, I have determined that a large number of these genes containing TE sequence are also expressed. This bioinformatic study used experimentally-derived Expressed Sequence Tag (EST) sequences, to confirm the TE-gene chimaera’s expression and to add a robust layer of “real-world” data. However, since TEs can sometimes pick up gene fragments, as well as insert into genes, I used the phylogenetic histories of gene families in the Arabidopsis genome to determine the direction of sequence transmission and to infer with confidence whether an actual insertion event took place or not. This paper is currently in preparation and will be submitted this summer.

The model plant Arabidopsis thaliana and its close relative Arabidopsis lyrata possess different mating systems. The former is highly selfing, while the latter is an obligate outcrosser. Population genetics theory predicts that recombination rates are lower in selfers compared to outcrossers and that selection is weaker in areas of low recombination. TE copy number can be maintained in genomes by either purifying selection acting against deleterious insertions, or by selection acting against harmful non-homologous recombination. Using a method called Transposon-Insertion Display (TID) I have gathered a large TE insertion frequency dataset for eight different TE families across both species, in 47 ecotypes per species. Using these data I will be able to tease apart the relative contributions of selection and recombination in controlling TEs in plant genomes, hence shedding more light on the structure and evolution of plant genomes themselves.

My final project of my Ph.D. thesis studies the effect of TE insertion on gene expression. TE polymorphism data was gathered for 22 genes from 48 A. thaliana ecotypes where the TE had inserted close to a gene (< 300 b.p.). One would hypothesise if a TE (often with its own promoters) landed in the regulatory region of a gene it would have an effect upon the expression of that gene. I intend to investigate this by producing F1 hybrids that contain one allele with the TE absent, and another with the nearby TE present. I will then measure the relative expression of both alleles. Using F1 hybrids will allow me to infer cis-regulatory change, as both alleles will exist in the same trans-factor background, which would be consistent with the hypothesis that TE insertion in promoters results in cis-regulatory change.