Human-specific signatures of the neuronal epigenome in PFC.

<p>(A) Pearson correlation coefficients (<i>R</i>, mean ± standard deviation [SD]) for sample-to-sample comparison of H3K4me3 ChIP-seq normalized tag counts within Refseq promoters, revealing cell type- and species-specific signatures. (B) Expected (blue)/observed (red) counts of human-specific H3K4me3 peaks (<i>n</i> = 410) overlapping with DNA hypomethylated regions in human (H)/chimpanzee (P) sperm. Notice 4-fold enrichment for loci with human-only (H+,P−) DNA hypomethylation in dataset <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001427#pbio.1001427-Molaro1" target="_blank">[19]</a>. (C) The actual co-localization of human-specific H3K4me3 peaks (<i>n</i> = 410) within 1- or 0.5-Mb genomic distance is 2–3-fold higher than expected (based on average distribution of entire set of 34,639 H3K4me3 peaks *⁽**⁾, <i>p</i><10⁻³⁽⁻⁴⁾. (D) Representative example of a TSS (<i>PDE4DIP/Myelomegalin</i> (“<i>regulator of brain size</i>”) with species- and cell type-specific H3K4me3 profile. Genome browser tracks showing ChIP-seq H3K4me3 signal at <i>PDE4DIP</i> (chromosome 1) locus, annotated to HG19/PT2/RM2 genomes as indicated. Green/blue/black tracks from PFC neuronal (NeuN+) nuclei of 11 humans/four chimpanzees/three macaques as indicated. Red tracks, non-neuronal (NeuN−) human PFC nuclei. Notice much stronger PDE4DIP peaks in human neurons.</p

H3K4me3 landscapes and higher order chromatin at the psychiatric susceptibility locus, 16p11.2.

<p>(Top) UCSC genome browser window track for approximately 1 Mb of human chr16: 21,462,663–22,499,013, with H3K4me3 ChIP-seq tracks from neuronal chromatin (PFC) of three primate species, as indicated. Notice human-enriched H3K4me3 peaks at chr16:21,512,663–21,514,196 and chr16:22,448,157–22,449,013 (marked by arrows) flanking numerous peaks common to all 3 species. (Bottom) Rectangles and thin arrows mark 3C HindIII restriction fragments and primers from 3C assays. Notice positive interaction of sequences captured by primers 2 and 7, agarose gels shows representative 196-bp PCR product for 3C from two PFC specimens (a,b), HEK cells, and no ligase and water controls.</p

Examples of disease-associated genes with human-specific gain or loss of H3K4 trimethylation in PFC neurons.

<p>ADHD, attention deficit hyperactivity disorder; LTD, long-term depression; NGF, nerve growth factor; PTSD, post-traumatic stress disorder.</p

H3K4me3 landscapes and higher order chromatin at <i>DPP10</i> (2q14.1).

<p>(A) (Top) Genome browser tracks showing ChIP-seq H3K4me3 signal at <i>DPP10</i> locus annotated to HG19 and RM2 genomes. Data expressed as normalized tag densities, averaged for 11 humans, four chimpanzees, and three macaques as indicated (see also <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001427#pbio.1001427.s001" target="_blank">Figure S1</a> for comparative annotation for each of the 18 specimens in HG19 at <i>DPP10</i>/2q14.1, and for the non-human primates also for the homologous loci in their respective genomes, PT2 and RM2). Human-specific peak <i>DPP10</i>-1 (1,455 bp) and <i>DPP10</i>-2 (3,808 bp) marked by arrows and shown at higher resolution in boxes, as indicated. (Bottom) Rectangles and arrows mark Hind III restriction fragments and primers from <i>DPP10</i>-1/2 (PK1, 2) and control regions (CR1-3) for 3C assays (human). Dotted lines connect primer pairs with sequence-verified product, indicating physical interaction of the corresponding fragments. Agarose gels for representative PCR products from 3C with (+) or without (−) DNA ligase (human primers 6,17: 282 bp; 6,18: 423 bp; 8,15: 160 bp; 9,15: 130 bp). (B) Rectangles and arrows mark Hind III restriction fragments and primers for corresponding DPP10 sequences in RM2, for macaque brain 3C. Macaque primers 6,12:298 bp, 8,12:154 bp. Notice positive interaction of PK1 with PK2 and neighboring CR2, but with not CR1 or CR3. Notice no signal in PFC 3C assays without DNA ligase and no signal in all 3C assays from H9 pluripotent (H9ESC) and differentiated (DIFF) cell cultures.</p