Positional cross correlations were calculated between reverse and forward CAGE tag 5’ ends at ChIP-seq derived active HeLa-S3 and GM12878 enhancer center positions (as determined by P300 peaks) +/−300 bp (max lag 300) to identify their most likely separation. Cross correlations were also calculated in 300 bp windows (max lag 150) flanking the enhancer centers between CAGE 5’ ends and ENCODE H2A.Z signals (from the same cell line) for HeLa-S3 and GM12878 as well as between CAGE 5’ ends and ENCODE GM12878 nucleosome MNase-seq 5’ ends (9 pooled replicates). In the latter analysis, correlations were made using reads on the same strand. Pooled, unique CAGE tags (in which only one CAGE tag per bp was counted) were considered in all correlation analyses and enhancers were weighed according to the aggregated signal before subsequent averaging over lags not to make any library or enhancer have an undue influence.
