Heterochromatin is a very compact region of DNA in which genes in these regions are generally not transcribed. Many 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 these TEs and DNA repeats (Lippman et al., 2004). Heterochromatin is capable of maintaining internucleosomal interactions as well as chromatin fiber interactions between cis elements. It can be passed on to subsequent generations and control gene expression by inhibiting transcription epigenetically, a process known as silencing. Heterochromatin is capable of suppressing recombination between interspersed DNA repeats. This prevents non-homologous recombination, which can lead to copy number variations in gene clusters and give rise to genetic diseases. In flowering plants like Arabidopsis (which will be the main focus of this essay), cytosine methylation is abundant in heterochromatic regions, and plays an important role in the 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 may 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 driven 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 into the cytosi...... middle of paper ......aeppler SM. 2001. Maize chromomethylase zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13:1919–1928.11 Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J 2003. Erasure of CpG methylation in Arabidopsis alters histone H3 methylation patterns in heterochromatin . Proc Natl Acad Sci USA 100: 8823–8827.12 Teixeira FK, Heredia F, Sarazin A et al. 2009. A role for RNAi in the selective correction of DNA methylation defects. Science 323: 1600–1604.13 Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T. 2009. Retrotransposition bursts reproduced in Arabidopsis. Nature 461:423–426.14 Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilbermann D. 2013. The Arabidopsis nucleosome remodeler DDM1 enables DNA methyltransferases to access heretrochromatin containing H1. . Cell 153; 193-195.