Heterochromatic marks are associated with presence of retrotransposons.

<p>(A) Whole genome shotgun sequence data for Mo17 was used to identify retrotransposon insertions that are present within the B73 haplotype but missing in Mo17. The relative level of DNA methylation at the probe nearest the empty site was assessed in B73 and Mo17 for empty sites of spreading (both) and for spreading (H3K9) retrotransposon families. For each set of families we compared the distribution of methylation patterns to a similar number of insertion sites that are conserved in both B73 and Mo17. (B) The DNA methylation levels for four of these “empty” sites (the coordinates specify the retrotransposon present in B73) are shown for two tissues of B73 (blue bars) and Mo17 (red bars) as well as for a single tissue of five other maize genotypes; CML228, CML277, Hp301, Tx303 and Oh7b (pink bars). Black bars for all genotypes indicate depletion of methylation signal. The location of the retrotransposon and its presence or absence are indicated by + or − symbols, respectively. The genotypes containing the insertion of the retrotransposon all exhibit enrichment for DNA methylation while the genotypes without the insertion do not. The “*” indicates probes with significantly (P<0.01) higher DNA methylation levels in B73 relative to the same tissue in Mo17. The horizontal gray line indicates the genome-wide average for each of the modifications. Higher values indicate higher levels of DNA methylation and all plots are show on the same scale for the y-axis. The scale for black line near the bottom of each plot indicates the base pair scale for the x-axis.