High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

Abstract

We present high-resolution maps of DNA methylation and H3K4 di-and trimethylation of two entire chromosomes and two fully sequenced centromeres in rice (Oryza sativa) shoots and cultured cells. This analysis reveals combinatorial interactions between these epigenetic modifications and chromatin structure and gene expression. Cytologically densely stained heterochromatin had less H3K4me2 and H3K4me3 and more methylated DNA than the less densely stained euchromatin, whereas centromeres had a unique epigenetic composition. Most transposable elements had highly methylated DNA but no H3K4 methylation, whereas more than half of protein-coding genes had both methylated DNA and di-and/or trimethylated H3K4. Methylation of DNA but not H3K4 was correlated with suppressed transcription. By contrast, when both DNA and H3K4 were methylated, transcription was only slightly reduced. Transcriptional activity was positively correlated with the ratio of H3K4me3/H3K4me2: genes with predominantly H3K4me3 were actively transcribed, whereas genes with predominantly H3K4me2 were transcribed at moderate levels. More protein-coding genes contained all three modifications, and more transposons contained DNA methylation in shoots than cultured cells. Differential epigenetic modifications correlated to tissue-specific expression between shoots and cultured cells. Collectively, this study provides insights into the rice epigenomes and their effect on gene expression and plant development.

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

“…Histone acetylation and methylation of H3K4 and K3K36 have been well documented to be associated with active genes. The patterns of the four histone modifications associated with rice genes were highly similar to those previously reported from both plant (Li et al, 2008;Wang et al, 2009;He et al, 2010) and mammalian species (Barski et al, 2007).…”

Identification and Characterization of an Epi-Allele of FIE1 Reveals a Regulatory Linkage between Two Epigenetic Marks in Rice

“…ChIP assays were performed as described previously (Nagaki et al, 2004;Li et al, 2008;Lu et al, 2011) with minor modifications. Approximately 2 g leaves of the 3-week-old rice seedlings was ground to fine powder with liquid nitrogen, resuspended in 37 mL of 1% formaldehyde in extraction buffer I (0.4 M Suc, 10 mM Tris-HCl, pH 8, 10 mM MgCl 2 , 5 mM a-mercaptoethanol [a-ME], 0.1 mM phenylmethylsulfonyl fluoride [PMSF], and proteinase inhibitors [Complete; Roche Molecular Biochemicals]), inverted gently and thoroughly to release the nuclei, and then stopped the cross-linking by adding Gly to a final concentration of 0.125 M. The solution was filtered through Miracloth (Calbiochem; catalog no.…”

Two Distinct Roles of ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1) at Promoters and within Transcribed Regions of ATX1-Regulated Genes

“…The genome-wide distribution of the H3K4me3 mark displays a predominantly gene-associated pattern with a strong bias toward the 59-ends of actively transcribed genes, in yeast (Ng et al, 2003), animal (Wang et al, 2009), and plant genomes (Li et al, 2008;Zhang et al, 2009;van Dijk et al, 2010). The mechanisms determining H3K4me3 distribution, as well as its role in transcription, are still emerging (Kouzarides, 2007;Shilatifard, 2008;Cazzonelli et al, 2009;Shukla et al, 2009).…”