Chen, Meng (2005-12). Disruption of DNA methylation induces genome-specific changes in gene expression in Arabidopsis allotetraploids. Master's Thesis.
Allopolyploids are formed by the combination of evolutionarily-diverged genomes, the
union of which leads to dynamic changes in gene expression and genome organization.
Expression patterns of orthologous genes are rapidly and stochastically established in
newly created allotetraploids, where gene silencing is maintained by microRNAs, DNA
methylation, and other chromatin modifications. Among them, DNA methylation has
been known as an important mechanism of epigenetic regulation of gene expression and
chromatin structure. However, it is unclear how DNA methylation affects genome-wide
expression of homoeologous genes in the natural polyploid Arabidopsis suecica that
contains genome of both A. thaliana and A. arenosa.
To understand the role that DNA methylation plays in the polyploidization process,
a comparative analysis was performed comparing up- or down-regulated genes in
met1-RNAi A. suecica lines with the non-additively expressed genes in the synthetic allotetraploids,
i.e., different from the mid-parent value. The previous studies indicated
that decreased DNA methylation in A. suecica induces A. arenosa-specific demethylation in centromere regions and differentially alters expression of >200 genes encoding
many transposons, unknown proteins and some other functional proteins that are located
along chromosomes, whereas >1,300 non-additively expressed genes in the synthetic
allotetraploids are distributed randomly along the chromosomes and encode various proteins
in metabolism, energy, cellular biogenesis, cell defense and aging, and hormonal
The origins of the progenitors of the genes whose expressions are altered in both
met1-RNAi A. suecica and resynthesized allotetraploid were analyzed with single strand
conformation polymorphism (SSCP) analysis. Reactivated genes in met1-RNAi A.
suecica lines were predominately derived from the A. thaliana genome in euchromatic
regions, whereas the suppressed genes were mainly derived from the A. Arenosa genome,
indicating that changes in DNA methylation are genome-sensitive. The data suggest that
allotetraploids incidentally display chromosome-specific changes and genomedependent
regulation of homoeologous genes in response to DNA methylation perturbations.