Co-evolutionary relationship between mobile DNA and eukaryotes : an insight from genome-wide characterization of MUTATOR (Mu)-like elements (MULEs) in Arabidopsis thaliana and Oryza sativa

• Main Author: Yu, Zhihui, 1963-
• Other Authors: Buyeau, Thomas E. (advisor)
• Format: Others
• Language: en
• Published: McGill University 2004
• Subjects: Arabidopsis thaliana > Molecular genetics.; Rice > Molecular genetics.; Transposons.
• Online Access: http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=84857

The sequencing of eukaryotic model organisms has provided us an unprecedented opportunity for a genome-wide characterization of Transposable Elements (TEs) and the study of TE-host relationships. By developing methodologies on database mining, we explored the existence of MUtator (Mu)-Like Elements (MULEs) in Arabidopsis thaliana and Oryza sativa. Mu elements were first discovered in Zea mays; so far, a dozen of the elements have been identified in the genome. We identified a total of 1392 MULEs from the sequenced Arabidopsis genome. They represent one of the most abundant, diversified, yet still mobile DNA transposon families in eukaryotes. The Arabidopsis MULEs are composed of not only the elements showing the typical Mu-family-specific terminal structure (that is the long Terminal Inverted Repeat, TIR), but also a novel type of non-TIR MULEs. Some of this latter type of elements was found to be active both transcriptionally and transpositionally. To understand host-mediated genome-wide regulation(s) on the MULE system in Arabidopsis, we characterized 235 MULE mobility-specific genes (or mudrA-like genes) by mapping them on the sequenced Arabidopsis chromosomes and performing a genome-wide expression assay utilizing Arabidopsis METHYLTRANSFERSE1 (MET1) mutant (met2) plants, we showed that MET1-mediated global CpG methylation can only repress a portion of the gene family; its efficiency depends largely on the gene locations within the context of Arabidopsis chromatin remodeling: stronger in heterochromatic regions but weaker in euchromatic ones. This finding suggests that the Arabidopsis heterochromatic regions are not just a graveyard for the accumulation of defective elements; rather, they may have been playing an important role on the repression of TE activity via, at least in part, exerting MET1-mediated silencing effect. Our expression analysis also suggested that a TIR structure is not necessarily required for the MET1-mediated si