Chen, Meng (2005-12). Disruption of DNA methylation induces genome-specific changes in gene expression in Arabidopsis allotetraploids. Master's Thesis. Thesis uri icon

abstract

  • 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
    regulation.
    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.

publication date

  • December 2005