Local and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis

Taiko Kim To (), Chikae Yamasaki, Shoko Oda, Sayaka Tominaga, Akie Kobayashi, Yoshiaki Tarutani and Tetsuji Kakutani ()
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Taiko Kim To: The University of Tokyo
Chikae Yamasaki: The University of Tokyo
Shoko Oda: The University of Tokyo
Sayaka Tominaga: The University of Tokyo
Akie Kobayashi: National Institute of Genetics
Yoshiaki Tarutani: National Institute of Genetics
Tetsuji Kakutani: The University of Tokyo

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: Abstract Transposable elements (TEs) are robustly silenced by multiple epigenetic marks, but dynamics of crosstalk among these marks remains enigmatic. In Arabidopsis, TEs are silenced by cytosine methylation in both CpG and non-CpG contexts (mCG and mCH) and histone H3 lysine 9 methylation (H3K9me). While mCH and H3K9me are mutually dependent for their maintenance, mCG and mCH/H3K9me are independently maintained. Here, we show that establishment, rather than maintenance, of mCH depends on mCG, accounting for the synergistic colocalization of these silent marks in TEs. When mCG is lost, establishment of mCH is abolished in TEs. mCG also guides mCH in active genes, though the resulting mCH/H3K9me is removed thereafter. Unexpectedly, targeting efficiency of mCH depends on relative, rather than absolute, levels of mCG within the genome, suggesting underlying global negative controls. We propose that local positive feedback in heterochromatin dynamics, together with global negative feedback, drive robust and balanced DNA methylome patterning.

Date: 2022
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DOI: 10.1038/s41467-022-28468-5

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