ChIP–chip analysis to identify genes with changes in the H3K27me3 levels between leaf and callus.

<p>(A) Leaf explants (left) and calli (right) were used for the ChIP-chip experiment. For preparation of experimental materials, leaf explants that were just cut from leaves of 20-day-old wild-type Col-0 seedlings and calli that were on the margins of leaf explants cultured on CIM for 20 days were harvested for nuclei extraction. (B) A comparison of H3K27me3 covered loci taken from three independent genome-wide analyses (seedlings from Zhang et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002911#pgen.1002911-Zhang1" target="_blank">[13]</a>, and leaves and calli in this work). (C) Classifications by annotated functions of the identified H3K27me3-covered genes with either decreased (left) or increased (right) levels. (D) Expression profiles of the genes identified by the ChIP-chip experiment with the decreased (left) or increased (right) H3K27me3 levels. The original expression data were downloaded from the online program Genevestigator <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002911#pgen.1002911-Hruz1" target="_blank">[30]</a>.