The proteins CMT3, UHRF1 and ESP1 repress select transposable elements in the model plant Arabidopsis thaliana

Abstract

Transposable elements (TEs) are mobile fragments of DNA that occupy large portions of eukaryotic genomes and can harmfully mutate the genome when they are active. To suppress TE activity, eukaryotic cells repress TE transcription using multiple elaborate mechanisms that are not well understood. The Autumn 2013 Molecular Genetics 5601 Laboratory course aimed to discover specific proteins in the plant Arabidopsis thaliana which act to maintain the epigenetic silencing of multiple TEs. In half of a semester we successfully genotyped 17 homozygous mutants, measured the expression of seven different TEs by qRT-PCR in these confirmed mutant lines, and additionally investigated the DNA methylation levels of specific mutant-TE combinations by McrBC-PCR. From our analysis we identified three proteins that function to suppress TE transcription. We unexpectedly found that the putative mRNA-binding protein ESP1 functions to maintain the silencing of particular select types of TEs, and the DNA methylation mutants cmt3 and uhrf1 have only minor reactivation of specific TEs, not a genome-wide global TE activation as previously suggested. Our data demonstrates that an undergraduate laboratory course can successfully identify new proteins involved in the repression of TEs while learning the fundamentals of molecular genetics and experimental biological research.