Fig. 7

Methylome analysis of seeds h2a.x maternal and WT paternal plant crosses. Genome-wide methylation analysis of h2a.x mutant developing embryo and endosperm, comparing maternal and paternal alleles in wild-type (WT) and h2a.x mutant crosses whereby the maternal allele is either WT Columbia or h2a.x homozygous mutant Columbia, and the paternal allele is always wild-type Ler; ‘h2a.x paternal’ denotes a wild-type paternal allele now resident in a heterozygous h2a.x mutant seed. (a) Fractional methylation difference between h2a.x double mutant gametophyte crossed with Ler WT pollen in CG methylation from embryo (linear-bending cotyledon) is plotted, data in 50 bp windows with > 20 × sequence coverage. (b) As for a, but with endosperm. A slight shift towards the left can be seen for the maternal endosperm allele (inherited from h2a.x mutant central cell). (c) Ends analysis of maternal (h2a.x mutant) genomic methylation in genes, with genes aligned according to their 5’ and 3’ ends. (d) Ends analysis of paternal genomic methylation in genes, with genes aligned according to their 5’ and 3’ ends. (e) Ends analysis of maternal (h2a.x mutant) genomic methylation in transposons, with transposons aligned according to their 5’ and 3’ ends. (f) Ends analysis of paternal genomic methylation in transposons, with transposons aligned according to their 5’ and 3’ ends. (g) Fractional CG DNA methylation difference between mutant and WT maternal endosperm in developing seeds from both hta3/hta3 hta5/ + (H2A.X-g3) and hta5/hta5 hta3/ + mutants (H2A.X-g5) were crossed to Ler, so that the sporophyte had one remaining copy of one of the isoforms, but both H2A.X isoforms are lost in ½ of the gametophytes. H2A.X-g5 and H2A.X-g3 are plotted alongside h2a.x. For both H2A.X-g3 and H2A.X-g5, the curve peaks are close to zero, whereas the full h2a.x mutant is skewed to the left, indicating redundancy between HTA5 and HTA3 isoforms in the context of mutant endosperm DNA hypomethylation