Gene Body CG and CHG Methylation and Suppression of Centromeric CHH Methylation are Mediated by DECREASE IN DNA METHYLATION1 in Rice Hisataka Numa, Katsushi.

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Gene Body CG and CHG Methylation and Suppression of Centromeric CHH Methylation are Mediated by DECREASE IN DNA METHYLATION1 in Rice Hisataka Numa, Katsushi Yamaguchi, Shuji Shigenobu, Yoshiki Habu Molecular Plant Volume 8, Issue 10, Pages 1560-1562 (October 2015) DOI: 10.1016/j.molp.2015.08.002 Copyright © 2015 The Author Terms and Conditions

Figure 1 Epigenomic Characteristics in Cytosine Methylation in asDDM1. (A) Genome-wide changes in cytosine methylation of chromosome 1 in asDDM1. Top two rows, methylation rate of CG (left), CHG (center), and CHH (right) sites in wild-type (black) and asDDM1 (red). Schematic figures of chromosome 1 with a black oval indicating the position of the centromere are shown above the panels. Middle two rows, differentially methylated regions (DMR) of CG (left), CHG (center), and CHH (right), respectively, between wild-type and asDDM1. Cytosines with significantly higher levels of methylation (FDR <0.01) in wild-type (black) or asDDM1 (red) per 100 kb windows are plotted. Bottom row, density of genes (left), transposable element (TE)-related genes (center), and repeats (right). Annotations for genes, TE-related genes, and repeats were taken from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/). (B) Methylation rates of CG (top), CHG (middle), and CHH (bottom) in the centromeric region in wild-type (black) and asDDM1 (red) are indicated against density of genes (left), TE-related genes (center), and repeats (right) in 10-kb windows. (C) Correlation between the methylation rate and expression in leaves. Methylation rates were calculated for 2 kb upstream (left), gene body (center), and 2 kb downstream (right) regions. Methylation rates are plotted for wild-type (black) and asDDM1 (red) against expression levels of the corresponding genes in leaf. (D) Correlation between methylation rate and expression variance. Methylation rates were calculated for 2 kb upstream (left), gene body (center), and 2 kb downstream (right) regions. Methylation rates are plotted against expression variance of corresponding genes as in (C). Molecular Plant 2015 8, 1560-1562DOI: (10.1016/j.molp.2015.08.002) Copyright © 2015 The Author Terms and Conditions