Figure 1
From: PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression
PHF8, REST and E2F1 bind at genome-wide promoters.
(A) Motif search of the highest-confidence PHF8 binding sites. Motifs in PHF8 binding sites surrounding gene promoters were searched. The REST motif was enriched in immortalized human cell lines HeLa, 293T, Hs68 and K562. (B) PHF8 and E2F1 are strongly enriched and REST is slightly enriched in gene promoters. Promoters, including 3 kb around the transcription start site and 5′UTR, were analyzed for PHF8, E2F1 and REST binding. Y-axis indicates the percentage of each region in the genome. (C) Overlap of PHF8, REST and E2F1 target genes. Venn diagram shows the overlap of genes targeted by PHF8 (red), REST (blue) and E2F1 (green) in HelaS3 cells, with the number of genes indicated in each area. The significance of overlap (p < 1.9e-266) was calculated using hypogeometric distribution. (D) PHF8, REST and E2F1 bind across the RPS3 locus. The height of the profile indicates the number of sequenced reads, showed in y-axis. (E) PHF8, REST and E2F1 co-occupy the genome. PHF8, REST and E2F1 ChIP-seq profiles of 5,506 PHF8 target genes (y-axis) in a 6-kb window centered on gene transcription start sites. Expression box depicts expression trend using average sliding window with steps equaling 100. The far-right box shows the distribution of PHF8 up-regulated (red) and down-regulated (blue) genes.
