Global correlation matrix of higher order chromatin datasets.

<p>The heatmap and dendrogram show the relationships among 36 chromatin structure datasets (Spearman's rho: 0.38 to 0.98, p<1e-16). Datasets are labelled according to the experimental platform of origin: light grey = mouse RT, light pink = human RT, dark grey = mouse LA, medium pink = human LA, dark pink = human Hi-C.</p

Chromatin divergence and GC content.

<p>Percentage of GC nucleotides within all 16,820 100 Kb orthologous regions across the spectrum of mean normalised chromatin structure values. The GC content and higher order structure values for human (left panel) are compared with the GC content and higher order structure values for mouse (right panel). Three classes of regions are shown with their least squares regression lines: nondivergent (grey), divergent open (blue) and divergent closed (red). Note that the bipolar classification of orthologous divergent regions (see text) means that human divergent open regions correspond to mouse divergent closed regions, and vice versa.</p

Chromatin divergence and expression divergence.

<p>Distributions of log2 fold change (log2(human/mouse expression)) for orthologous gene pairs within nondivergent regions (grey) and two classes of divergent regions: open in human but closed in mouse (blue), closed in human but open in mouse (red). For each class the bottom and top of the box show the lower and upper quartiles respectively around the median, and the width of the notches is proportional to the interquartile range.</p

Specific human and mouse regions show significant divergence in higher-order chromatin structure.

<p>Human (pink) and mouse (grey) higher order chromatin structure across all cell types assayed, shown for two regions of the human genome: chromosome 11p15.2–15.4 (1.2–15 Mb) with the location of an OR gene cluster indicated by an asterisk (A); chromosome 7p14.3–15.3 (24–32 Mb) with the location of the HOXA gene cluster indicated by an asterisk (B). In each case the chromosome ideogram indicates the region expanded in the heatmaps with a square bracket. Consecutive, orthologous 100 kb regions are positioned on the y-axis with heatmap colours representing relatively open (blue) and closed (red) chromatin structures. Regions displaying significantly divergent chromatin structure are highlighted in yellow.</p

The top 5 enriched human annotation terms for genes within large regions of divergent higher order chromatin.

<p>The top 5 enriched human annotation terms for genes within large regions of divergent higher order chromatin.</p

Clustering of divergent chromatin in the human genome.

<p>The line plot shows mean normalised human (black) and mouse (red) higher order chromatin structure values across human chromosomes. Unexpectedly large divergent areas are highlighted in grey. Asterisks indicate the positions of functionally enriched gene clusters listed in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003017#pcbi-1003017-t002" target="_blank">Table 2</a>.</p

The top 5 enriched human and mouse annotation terms for genes within divergent regions of higher order chromatin.

<p>The top 5 enriched human and mouse annotation terms for genes within divergent regions of higher order chromatin.</p

H2A.Z maps to Hox loci in wild-type and PRC1 mutant ESCs.

<p>Log2 of ChIP:input for: H2A.Z, H3K27me3, EZH2 and Ring1B from WT (+/+) (top) and <i>Ring1B^−/−</i> (bottom) ESCs using a custom tiling microarray. Data is shown for the four paralogous murine hox loci (Hoxa, Hoxb, Hoxc and Hoxd) and their flanking genomic regions. The data represent a mean of 2 biological replicates. RefSeq gene annotations and CGIs are from the July 2007 (mm9) Build 37 assembly of the mouse genome (genome.ucsc.edu).</p

Psip1 PWWP domain binds to H3K36me3.

<p>A) Diagram of p52 and p75 Psip1 isoforms showing the position of the; PWWP domain, AT hook-like domains (hatched box), C-terminal 8 a.a. unique to p52 (black box), and the p75-specific IBD. Vertical arrow indicates the site of gene trap integration in <i>Psip1^gt/gt</i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002717#pgen.1002717-Sutherland1" target="_blank">[22]</a>. Horizontal lines indicate the position of epitopes recognized by antibodies A300-847 and A300-848. B) Peptide array containing 384 histone tail modification combinations incubated with GST-Psip1-PWWP and detected with αGST. Spots corresponding to unmodified H3 26–45 peptide (arrow) and H3K36me3 (arrowhead) are indicated. C) Binding specificity (calculated from the intensity of the histone peptide interaction) of Psip1-PWWP (y axis) to the top list of histone modifications arranged according to decreasing specificity (x axis). Data for all the modifications are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002717#pgen.1002717.s002" target="_blank">Table S1</a>. D) Immunoblot of biotinylated H3K36me3 peptide pull-down detecting GST-p52 with αGST antibodies. Corresponding unmodified histone H3 peptide served as control and GST-p52 was loaded as input. E) Immunoblot of A300-847 IPs with antibodies detecting; unmodified H3, H3K36me3, H3K9me2 and H3K4me3. IgG served as control and 5% of NIH3T3 nuclear extract was loaded as input.</p

Sub-cellular localization of Psip1/p52 and p75.

<p>A) Immunofluorescence and wide-field epifluorescence microscopy on human cells with; (upper row) p75-specific antibody A300-848, (lower row) A300-847 which can recognize both p52 and p75. DNA was counterstained with DAPI. B) Co-immunofluorescence of Psip1/p52 (green/A300-847) and SRSF2 (red) analyzed by confocal microscopy in untreated (upper row), or actinomycin D (ActD) treated cells. C) Co-immunofluorescence of Psip1/p75 (green/A300-848) and SRSF2 (red) in ActD treated cells and analyzed by confocal microscopy.</p