Heterochromatin is a tightly packed DNA region where genes in such regions are usually not transcribed. Numerous transposable elements (TEs) and repetitive DNA are found in heterochromatic regions. As they can transpose along the genome and disrupt gene functions, it is essential to repress such TEs and DNA repeats (Lippman et al., 2004).
Heterochromatin is able to maintain internucleosomal interactions as well as chromatin fiber interactions between cis-elements. It can be passed on to subsequent generations and can control gene expressions by inhibiting transcription epigenetically, a process known as silencing. Heterochromatin is able to suppress recombination between interspersed DNA repeats. This prevents non-homologous recombination, which may result in copy number variations in gene clusters and give rise to genetic diseases.
In flowering plants like Arabidopsis (which will mainly be the focus of this essay), cytosine methylation is abundant in heterochromatic regions, and plays an important role in epigenetic regulation of genomes. DNA methylation in such genomes can affect cytosine residues in 3 different contexts: CG, CHG and CHH, where H can be C, T or A. One can wonder how these methylations are maintained in plant genomes. This can be explained by the dimethylation activity of cytosine-DNA methyltransferases on histone H3 at lysine 9(H3K9).
DNA methylation is initiated by RNA-directed methylation (RdDM), a process which is led by small and long non-coding RNAs via the Dicer-Argonaute pathway (Dinh et al., 2013). Once DNA methylation is initiated, it must be maintained to effectively suppress gene transcription in heterochromatin.
Cytosine-DNA methytransferases are enzymes that introduce a methyl group to cytosine in dsDNA, generating C5-methylcytosine. After DNA replication, these enzymes bind to hemi-methylated cytosines (from the parent strand) and methylate newly synthesized DNA strands. This helps maintain cytosine methylation patterns throughout cellular divisions.
Maintenance of CG methylation sites
In Arabidopsis, the enzyme METHYLTRANSFERASE1 (MET1) maintains CG site methylations (Du et al., 2012), together with 3 Variant In Methylation (VIM1 – 3) genes. Met1 mutants showed severe loss of H3K9 methylation in CG regions (Tariq et al., 2003).
VIM1, a methylcytosine –binding protein, attaches itself to methylated cytosine at CG sites through the SRA domain. This binding aids the recruitment of MET1, which results in methylation of the newly synthesized daughter DNA strand.
Deficient In DNA Methylation I (DDM1), an enzyme involved in modifying the chromatin structure, has been found to be involved in CG maintenance methylation (Gendrel et al., 2002). Recessive ddm1 mutants seem to show increased transposition of some LTR retrotranspons, which may be due to drastic loss of DNA methylation (Tsukahara et al., 2009). Ddm1 Arabidopsis crossed with its WT counterpart continued to show severe loss of DNA methylation...