Chromatin Conservation and Divergence For Paralogs In Maize

Chromatin modifications, such as DNA methylation and histone methylation, can provide regulatory information in addition to DNA sequence.  We have profiled the patterns of DNA methylation and H3K27me3 in several tissues and genotypes of maize.  There is evidence for substantial natural variation for DNA methylation patterns between different genotypes of maize and for many tissue-specific differences in H3K27me3 distribution.  The analysis of genes that are targeted by H3K27me3 in maize, rice and Arabidopsis reveals substantial conservation of the targets of this modification in plants.  The maize genome underwent a whole-genome duplication event that results in the presence of two sub-genomes and ~30% of genes have retained copies in both sub-genomes.  There is limited evidence that either DNA methylation or H3K27me3 contributes to distinction between the two sub-genomes of maize.  The average abundance of these marks is similar in the two sub-genomes.  There is limited evidence for conserved targeting of H3K27me3 paralogs.  Instead, this mark is often found for only one of the two paralogs in a specific tissue.  The differences in tissue-specific distribution of H3K27me3 for paralogs suggests that H3K27me3 has the potential to contribute to sub-functionalization via tissue-specific regulation.