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. 2019 Apr 24;47(11):5573–5586. doi: 10.1093/nar/gkz272

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — PTEN binds to chromatin in promoter and putative enhancer regions. (A) PTEN ChIP-seq meta-profiles using two PTEN antibodies in PTEN WT (blue) and CRISPR-PTEN (red) HeLa cells. Data are centered and ±1 kb are shown. Plots represent average read counts per 50 bp bins. (B) Representative captures of the UCSC genome browser (GRCh37/hg19) showing PTEN, and publicly available RNAPII (44,45), H3K27ac, H3K4me1 and H3K4me3 (46,47) tracks in HeLa cells. The y-axis represents normalized read counts in reads per million. (C) Heatmaps of ChIP-seq reads for PTEN, and publicly available RNAPII (44,45), H3K27ac, H3K4me3 and H3K4me1 (46,47). Data are centered and ±3 kb are shown for (top) 2495 promoter regions and (bottom) 938 distal regions rank-ordered by PTEN occupancy. (D) GO enrichment analysis of PTEN-bound genes. p-values are given. (E) Log₁₀FPKM of 3830 high, 7660 median, and 3830 low expressed genes, 2672 PTEN-bound and 2672 random genes in PTEN WT HeLa cells. Tukey boxplots with outliers omitted. Student's t-test, ****P ≤ 0.0001. (F) Hypergeometric gene set enrichment analysis to determine the overlap between differentially expressed and PTEN-bound genes. P-value and fold-enrichment are given. Calculation was based on 15 330 genes. (G) GO enrichment analysis of PTEN-bound genes that were significantly downregulated after PTEN loss. p-values are given.