Fig. 2: KLF regulates chromatin accessibility of vasculo-protective genes under LSS. | Nature Communications

Fig. 2: KLF regulates chromatin accessibility of vasculo-protective genes under LSS.

From: KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress

Fig. 2

a PAEC were transduced overnight with adenoviral vectors encoding caMEK5 or GFP as control. Ninety hours after transduction, chromatin accessibility changes were analyzed by ATAC-Seq and gene expression changes by RNA-Seq. Scatterplots show the correlation between changes in chromatin accessibility (left panel) and gene expression (right panel) in caMEK5 transduced PAEC compared to PAEC exposed to LSS. n = 3 experimental replicates. Indicated values were calculated by a two-tailed Pearson R test, with P < 0.0001. Each dot represents a differentially accessible region (left panel) or differentially expressed gene (right panel). b PAEC were treated with siRNA targeting KLF2 and KLF4 (siKLF), or non-targeting controls (SiC), 24 h prior to exposing the cells to 15 dyn/cm2 of LSS vs ST conditions for an additional 24 h. Chromatin accessibility changes were analyzed by ATAC-Seq and gene expression changes by RNA-Seq. Scatterplots show the correlation between changes in chromatin accessibility (left panel) and gene expression (right panel) in siKLF treated cells compared to untreated PAEC exposed to 15 dyn/cm2 of LSS for 24 h. n = 3 experimental replicates. Indicated values were calculated by a two-tailed Pearson R test, with P < 0.0001. Each dot represents a DAR (left panel) or DEG (right panel). c ATAC-Seq tracks showing a DAR upstream of DUSP5 with increased accessibility under LSS vs ST control (left panel). Bar graphs showing the ATAC-qPCR analysis of the DUSP5 DAR, and of DUSP5 mRNA transcript levels by RT-qPCR (right panel). d ATAC-Seq tracks showing increased accessibility of the DAR upstream of DUSP5 in PAEC transduced with caMEK5 vs GFP controls. Bar graphs of the ATAC-qPCR and RT-qPCR analyses of caMEK5 transduced PAEC as described above (right panel). e ATAC-Seq tracks of PAEC treated with siKLF as described above (left panel). Bar graphs of the ATAC-qPCR and RT-qPCR analyses of siKLF treated PAEC (right panel). For c–e, n = 3 experimental replicates. qPCR data are shown as the mean +/− s.e.m. P values were determined by Student’s two-tailed t-test. Source data are provided as a Source Data file.

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