ChIP-seq-based analysis of i) K27me3 promoter coverage and ii) enhancer elements in neuroblastoma cell lines. Homo sapiens

To investigate whether a set of differentially methylated/expressed genes, identified in neuroblastomas of differential outcome, co-localizes with K27me3 marks or enhancer elements, we performed H3K4me3, H3K4me1, H3K27ac and H3K27me3 ChIP seq in neuroblastoma cell lines. Overall design: Enhancers were defined in neuroblastoma cell lines as overlapping H3K4me1 and H3K27ac peaks with a minimal distance of 2 kb to the closest H3K4me3 peak, a criterion imposed to rule out selection of (unannotated) promoters. Promoter-near K27me3 coverage was also analyzed in neuroblastoma cell lines. The effect of MYCN on K27me3 occupancy was investigated upon modulation of MYCN levels.