ABSTRACT
RYO FUJIMOTO, TAKU SASAKI, RYO ISHIKAWA, KENJI OSABE, TAKAHIRO KAWANABE, and ELIZABETH S. DENNIS
12.1 INTRODUCTION
Variation in DNA sequence can cause variation in gene expression, which influences quantitative phenotypic variation in organisms and is an important factor in natural variation. Gene expression regulatory networks are comprised of cis-and trans-acting factors, and differences in gene expression are attributable to genetic variation. In eukaryotes, the genome is compacted into chromatin, and the chromatin structure plays an important role in gene expression: Gene expression can be controlled by changes in the structure of chromatin without changing the DNA sequence, and this phenomenon is termed “epigenetic” control. Recently, there have been many reports indicating that epigenetic change can cause phenotypic variation, and thus epigenetic change can be considered as an important factor in understanding phenotypic change. DNA methylation and histone modifications are well known epigenetic modifications. DNA methylation refers to an addition of a methyl group at the fifth carbon position of a cytosine ring, and in plants it is observed not only in the symmetric CG context but also in sequence contexts of CHG and CHH (where H is A, C, or T) [1-3]. DNA methylation is enriched in heterochromatic regions, such as in centromeric and pericentromeric regions, predominantly consisting
of transposons [3-7]. Most transposons are immobile to protect genome integrity and are silenced via DNA methylation [3,8-12]. DNA methylation is also observed in euchromatic regions such as gene-coding regions (gene body methylation), and it is widely seen in eukaryotes [3,13,14].
