DNA Replication and Heterochromatin

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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 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 patterns of histone H3 methylation 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. Bursts of retrotransposition reproduced in Arabidopsis. Nature 461: 423–426. 14 Zemach A, Kim M.Y, Hsieh P.H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer S.L, Zilbermann D. 2013. The Arabidopsis Nucleosome Remodeler DDM1 allows DNA methyltransfereases to access H1- containing heretrochromatin. Cell 153; 193-195.

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