Histone modification profiles at REST peaks.

<p>Profiles of (A) H3K4me3 and (B) H3K27me3 ChIP-seq signal at REST peaks in GM12878 cells, H1 ESCs, neurons, A549, HeLa S3, Hep G2, and K562 cells. Y-axis shows the read density from Zhu <i>et. al. </i><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003671#pcbi.1003671-Zhu1" target="_blank">[68]</a> or ENCODE <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003671#pcbi.1003671-A1" target="_blank">[34]</a> per 150 bp averaged over REST-bound peaks in each cell type from −6 kb to 6 kb of the peak summits. Data were normalized to a read depth of 5 million mapped reads.</p

Overlap of REST peaks with genomic regions enriched with histone modifications.

<p>Overlap of REST peaks with genomic regions enriched with histone modifications.</p

Colocalization of REST and its cofactors and their relationship with gene expression.

<p>(A) Venn diagram of colocalization of SIN3, COREST, and EZH2 at REST peaks. The square constitutes all REST peaks. (B) Context enrichment of REST peaks bound by different cofactors; fold enrichment is compared to all REST peaks. (C) Expression of REST targets with different cofactors, plotted as log2(FPKM+0.1); asterisks mark significant differences. Data shown here are for GM12878 and data for Hep G2 are in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003671#pcbi.1003671.s006" target="_blank">Figure S6</a>.</p

Numbers of REST peaks and REST-bound genes in each cell type.

<p>Numbers of REST peaks and REST-bound genes in each cell type.</p

Key neural miRNAs and factors regulated by REST.

<p>REST peaks for each gene or miRNA are shown as a cartoon, represented on two lines to indicate REST binding in neurons (N) and non-neuronal cells (NN). TSS is marked by a purple vertical line and direction of transcription indicated by arrows. Black lines indicate miRNA regulation. MiRNAs in purple, REST cofactors in green, transcription factors in pink and their actions on neural development indicated by blue arrows (activate) or flat lines (repress).</p

MiRNA transcript abundance (RPKMs).

<p>MiRNA transcript abundance (RPKMs).</p

REST binding in H1-neurons and T cells.

<p>(A) Top motifs identified in T cell ChIP-seq peaks by MEME: (top) cRE1 and (bottom) left and right half-sites of the ncRE1. (B) Distribution of peaks with RE1 motifs. (C) Genomic distribution of REST peaks. (D) Pathways enriched in the REST-bound genes in T cells and neurons, from GREAT <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003671#pcbi.1003671-McLean1" target="_blank">[39]</a>; data from “Pathway Commons” were shown and presented as fold enrichment (all p-values≤1.35E-15).</p

Heatmap of ChIP-seq read density across REST peaks.

<p>(A) Heatmap of maximal read coverage in 300 bp bins from −3.15 kb to +3.15 kb of the peak summits at all peaks identified from all 16 cell types (n = 21,134). The common peaks (top; n = 1,116), and cell-specific peaks (bottom; n = 6,003) are delineated from the remaining (middle; shared) peaks by red boxes and furthermore by blue boxes to demarcate cell-specific peaks for individual cell types. The labels for cell types are, A-A549, T-Tcell, E-ECC-1, G-GM12878, H1-H1 ESC, N-Neuron, Hc-HCT-116, Hel-HeLa S3, Hep-Hep G2, Hl-HL-60, K-K562, Pa-PANC-1, Pf-PFSK-1, S-SK-N-SH, U-U87. (B–D) Pileup of REST ChIP-seq reads mapped to three selected genes with common (B), shared (C), and cell-specific (D) peaks, as displayed in the IGV browser. In B–D, labels were used to mark cell types contained the peaks, as called by the SPP software.</p

Transcription of REST targets bound by REST in different contexts.

<p>(A) Comparison of the expression of REST-bound targets (b) vs. unbound REST candidate genes (ubrc; bound in other cell types except the subject one) or all genes (all). (B–D) Expression differences of REST targets: (B) with one peak vs. more peaks; (C) bound by peaks with cRE1, ncRE1, half-site or no RE1; (D) associated to common, shared, or cell-specific peaks. Asterisks mark significant differences in expression (p<0.05). Numbers in boxes are the number of genes whose peak has the specified context. Data plotted as log2(FPKM+0.1) and shown here for T cells, GM12878 cells, neurons and Hep G2 cells; data for other cells are in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003671#pcbi.1003671.s014" target="_blank">Table S6</a>.</p