Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing
Summary
Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited differential DNA methylation affects de novo targeting of chromatin modifiers in the early endosperm. Our data reveal that polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is preferentially localized to regions that are targeted by the DNA glycosylase DEMETER (DME), mechanistically linking DNA hypomethylation to imprinted gene expression. Our data furthermore suggest an absence of de novo DNA methylation in the early endosperm, providing an explanation how DME-mediated hypomethylation of the maternal genome is maintained after fertilization. Lastly, we show that paternal-specific H3K27me3- marked regions are located at pericentromeric regions, suggesting that H3K27me3 and DNA methylation are not necessarily exclusive marks at pericentromeric regions in the endosperm.
Overall design
Analysis of H3K27m3, H3k9m2 and H3K27m1 modifications and DNA methylation in endosperm and leaves in Arabidopsis. The ChIP-seq experiment consists of 37 samples. These include two replicates for each combination of cross/tissue/histone modification analyzed, except for the sample with H3k27m1 in leaf which has only one replicate. Most inputs and H3 samples are common for two or more H3-methylation samples. The BS-seq experiment consists of two samples that are replicates.
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