Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy

Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) and methylation of histone 3 on lysine 9 (H3K9me) are two repressive epigenetic modifications that are typically localized in distinct regions of the genome. For reasons unknown, however, they co-occur in some organisms and special tissue types. In this study, we show that maternal alleles marked by H3K27me3 in the Arabidopsis endosperm were targeted by the H3K27me3 demethylase REF6 and became activated during germination. In contrast, maternal alleles marked by H3K27me3, H3K9me2, and CHG methylation (CHGm) are likely to be protected from REF6 targeting and remained silenced. Our study unveils that combinations of different repressive epigenetic modifications time a key adaptive trait by modulating access of REF6. Overall design: Endosperm tissues were dissected from germinating seeds of Arabidopsis thaliana and analysed in two parallel experiments. Firstly, by comparing three replicates of wild type against three replicates of the ref6-1 mutant. Secondly, by comparing three new replicates of wild type against three replicates of the suvh456 mutant. Total RNA was extracted using MagMAX™ Plant RNA Isolation Kit (Thermo Fisher Scientific), and cDNA libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB). Libraries were sequenced on Illumina NovaSeq platforms as paired-end through Novogene mRNA sequencing services.