GSE105000
Genome-wide bisulphite sequencing of Arabidopsis thaliana embryo and endosperm
The DEMETER (DME) DNA glycosylase mediates genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-demethylation are small, AT-rich transposons and boundaries of large heterochromatic transposons, but how DME interacts with chromatin is unclear. To investigate the interaction between DME and chromatin, we analyzed DNA methylation in Arabidopsis seeds and pollen deficient in the chromatin remodeler FAcilitates Chromatin Transactions (FACT) complex. We find that FACT co-localizes with nuclear DME, and is required for DME activity in chromatin domains with high nucleosome occupancy and histone modifications associated with heterochromatin, which comprise over half of DME target loci. We also demonstrate that heterochromatin-associated linker histone H1 mediates the requirement for FACT at a subset of DME-target loci. However, FACT is not required for DME demethylation of targets in euchromatic regions.  Thus, chromatin structure determines the degree to which FACT facilitates access of DME to its targets. Overall design: DNA methylation was measured in pools of 50-100 hand-microdissected embryos and endosperm from Arabidopsis mutants and controls; FACS sorted Arabidpsis sperm and vegetative cell nuclei: mutants were ssrp1-3 plus sibling wild-type (two bioreplicates), spt16-3 plus sibling wild-type, h1.1 h1.2 ssrp1 triple mutants plus h1.1 h1.2 sibling controls