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. 2012 May 3;8(5):e1002658. doi: 10.1371/journal.pgen.1002658

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Wollmann et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) Smoothed density of H3 (blue), IgG (light grey), H3.1 (orange), H3.3 (green) and H3K9me2 (dark grey), a heterochromatin mark, over the complete chromosome 4. The heterochromatic knob and centromeric regions are shown as black bars. Note the anti-correlation of H3.3 and H3K9me2 at the heterochromatic knob and over the centromere. (B) Average profile of H3.3 (green), H3.1 (orange), H3 (blue), IgG (light dashed grey) and H3K9me2 (dark grey) over 20 Mb genomic regions of the five chromosomes, centered on the middle of their centromeres. The anti-correlation between H3K9me2 and H3.3 enrichment is general over all centromeres. (C–D) Boxplot representations of the average enrichment of H3.3 (green), H3.1 (orange), H3 (blue), IgG (light grey), H3K4me3 (purple) and H3K9me2 (dark grey). (C) Distribution over chromatin states defined by [37]: 1545 CS1 regions mostly associated with H3K4me3, H3K9me3 and H3K36me3 active marks, 1046 CS2 regions associated mostly with H3K27me3 and H3K27me2 repressive marks, 637 CS3 regions associated mostly with H3K9me2, H4K20me1 and H3K27me1 constitutive heterochromatin marks, and 2413 CS4 regions with no prevalent marks. H3.3 is preferentially associated with CS1 and less with CS3 whereas H3.1 is more uniformly distributed. (D) Distribution over all genomic features annotated in TAIR9: 27337 protein-coding genes (Genes), 4838 transposable elements and pseudogenes (TEs), 1392 other annotations (Others), and 32910 inter-annotation regions >150 bp (IRs). H3.3 enrichment is much lower than H3.1 over TEs, and both H3 variants are more associated with genes than with inter-annotation regions.