Transposable Elements

Abstract

The host laboratory focuses on “RNA silencing”, a universal mechanism of gene regulation mediated by small RNAs. In plants, one key function of RNA silencing is to mediate defense against invasive parasites such as viruses and transposable elements, the latter being the object of this course. The single project will be conducted in parallel by three groups of three students.

Objective

Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations; some copy themselves and increase in number within the genome. Though they may cause single-gene mutagenic events, the large scale chromosome rearrangements caused by TEs via illegitimate recombination is by far the main threat they pose to genome integrity. As a result, many organisms use epigenetic control, via DNA/histone methylation, to tame TEs because the ensuing heterochromatin is recalcitrant to recombination. How are active TEs initially detected by their hosts, how is their genomic proliferation arrested and DNA/histone methylation deposited specifically on their genomes; what are the long term - often paradoxically beneficial - consequences of this epigenetic silencing for the host will be addressed in this course, using the plant Arabidopsis thaliana as a model system.

Content

The course will cover many aspects of TE biology by following the fate of an epigenetically reactivated, single-copy retro-element of Arabidopsis called ÉVADÉ (EVD). EVD’s reactivation will be confirmed by methylation analysis of its Long-terminal repeat (LTR) promoter using bisulfite sequencing. We will then follow EVD’s proliferation in the Arabidopsis genome by quantifying its copy number over multiple inbred generations using quantitative PCR analyses. We will see how, when this number reaches a critical figure of 40-45, all copies of EVD become simultaneously silenced by LTR-derived silencing sRNAs, which we will quantify and map using Illumina deep-sequencing data. We will finally see the consequences of these successive events.

Resources