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. Author manuscript; available in PMC: 2016 Oct 20.
Published in final edited form as: Nature. 2016 Apr 20;533(7601):95–99. doi: 10.1038/nature17939

Extended data Fig. 7. PD-associated risk variants have little effect on enhancer-specific chromatin modifications at intron-4-enhancer.

Extended data Fig. 7

(a) Overview of isogenic cell lines (derived from WIBR3 hESCs) carrying distinct genotypes of the intron-4-enhacer element used for chromatin-immunoprecipitation (ChIP-qRT-PCR and ChIP-seq). (b, c) ChIP-qRT-PCR analysis in neurons derived from isogenic cell lines with indicated genotypes for binding of the enhancer-specific chromatin marks H3K4me1 (b) and H3K27ac (c) at the intron-4 and 3′UTR enhancer sequences compared with indicated negative control regions (calculated as percent of input). (d) Gene tracks of ChIP-seq analysis for the active enhancer mark H3K27ac in in vitro differentiated neurons derived from isogenic cell lines with indicated genotypes. (e) Quantitative read density analysis of H3K27ac Chip-seq data (as shown in d) displaying relative read density of the intron-4 enhancer compared to the 3′UTR enhancer to control for variability between ChIP experiments. Source data are provided as Source Data for Extended Data Figure 7.