Fig. 1: POU2AF2 elicits opposing effects of gene expression at distal enhancer elements.

a The POU2AF2 and POU2F3 ChIP-seq was conducted in human SCLC cell line NCI-H526 cells. The overlapping POU2AF2 and POU2F3 peaks (n = 6987) were divided into three clusters by k-means clustering based on POU2AF2, POU2F3, and histone marks (H3K4me1, H3K27ac, H3K4me3, and H3K27me3). The ChIP-seq signal of these histone marks were further centered on the three clusters. b The scatter plot shows the correlation of gene expression change when POU2F3 or POU2AF2 were depleted by sgRNAs. The significantly altered genes (|log2FC|>1, adj. p < 0.01) by POU2F3/POU2AF2 depletion were highlighted in red (upregulated, n = 774) or blue (downregulated, n = 406). Data are derived from two biological replicates. Genes with Benjamini-Hochburg adjusted p-values less than 0.01 were considered to be differentially expressed in the EdgeR analysis⁴⁸. c Metascape pathway enrichment analysis with up-regulated genes in both POU2F3 and POU2AF2 depleted cells. The -log10(P) value was calculated by Metascape software v3.5⁴⁹. d The heatmap shows the nearby gene expression change aligned to the corresponding ChIP-seq peak (Fig. 1a) in either POU2AF2 depleted, POU2F3 depleted, or JQ1 treated NCI-H526 cells. Data are derived from two biological replicates. e The Venn diagram shows the overlap between JQ1 target genes and POU2F3/POU2AF2 common target genes. f The enhancer regions marked by H3K4me1 and H3K27me3 (n = 6538), or H3K4me1 and H3K27ac (n = 35503) were identified in NCI-H526 cells. The motif analysis shows the most significant motifs enriched in each type of enhancer elements. HOMER screens its library of reliable motifs against the target and background sequences for enrichment, returning motifs enriched with a p-value less than 0.05⁵⁵. g The track examples show the occupancy of POU2F3 and POU2AF2 at H3K4me1 and H3K27me3 marked enhancer regions, and the activation of nearby gene expression upon the loss of POU2AF2.