Fig. 5 | Nature Communications

Fig. 5

From: Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma

Fig. 5

Validation of TEAD1-binding targets by chromatin immunoprecipitation. a Density plot of correspondence analysis between chromatin accessibility and gene expression. Plotted on the y-axis is the average rld-normalized gene expression for each gene from all RNA-seq E+GSC sample data. Plotted on the x-axis is the highest ATAC-seq peak associated with the proximal promoter [−5 kb, +3 kb] of the same gene. Color intensity indicates density of the gene population, with red representing higher densities and blue representing lower densities. Strong correspondence is observed between open chromatin peaks and a moderate/high level of gene expression in all E+GSC samples (plot for one representative sample shown here). Several putative TEAD1-target genes of interest are indicated on the plot. b IGV plot of ATAC-seq piled reads at EGFR, AQP4, and CDH4 in four different acutely sorted E+GSCs (D.PROM distal promoter of EGFR, peak180759: chr7:55,000,372–55,001,595; P.PROM proximal promoter to TSS of EGFR, peak180777: chr7:55,085,981–55,088,747). For this IGV representation, reads are centered on the cut site of the Tn5 enzyme, correcting for the 9 bp occupancy of Tn5, and presumed footprints/peak troughs corresponding to TEAD motifs are delineated by downward arrow. c Chromatin immunoprecipitation (ChIP-PCR) in GBM tissues. Significant enrichment of TEAD1 (but not TEAD4) over IgG is seen specifically at differential open chromatin peaks with associated TEAD1 motif within the upstream promoter of EGFR (D. PROM, chr7:55001141 motif start site) (n = 6, *p = 0.011), at CDH4 (chr20:60011935 motif start site) (n = 6, *p = 0.027), and at the proximal promoter of AQP4 (chr18:24444251 motif start site) (n = 6, *p = 0.029). Significant binding above background is not observed at EGFR P.PROM or at chromatin inaccessible regions (IN2 = EGFR intron 2). Enrichment is expressed as fold increase over IgG, after normalization with 10% input, using 2^–ΔΔCt analysis accounting for primer efficiency: (E^IA−S)sample/(E^IA−S)IgG. E: primer efficiency; IA: 10% Input-Adjusted Ct; S: sample Ct. Bars represent mean ± SEM. d Western immunoblot illustrates decreased expression of AQP4 and CDH4 in TEAD1KO but not in TEAD4KO G-13063 GBM cells

Back to article page