Fig. 1

Overlapping dinucleosomes are enriched at gene regulatory elements. (a) Metaplots depicting average OLDN occupancy over all gene TSSs in human HeLa cells (top, data from DRP003456 [21]) and murine ES cells (bottom, data from GSE183278 [36]). Each line represents the mean of two biological replicates. OLDNs were identified bioinformatically using a fragment size selection between 230–270 bp. HeLa cell data were size-selected by gel extraction between 200–300 bp, while murine ES cell data were size-selected bioinformatically. (b) OLDN occupancy over gene-distal DNaseI hypersensitive sites (DHSs, GSM1014154 [37]) as in (a). n = 2 (mean). Data were processed as in panel a. (c) Overlaid OLDN and mononucleosome metaplots depicting spatial relationships between nucleosome structures at gene-distal DHSs. Fragment size was used to distinguish mononucleosomes (red, 135–165 bp) and OLDNs (blue, 230–270 bp). n = 2 (mean). Data from HeLa cells (top) and ES cells (bottom), processed as in panel a. (d) Schematic of MNase-seq experimental workflow and OLDN enrichment process, where parallel libraries were generated from the same sample: one including all MNase-digested products (unextracted) and one enriched for OLDNs (gel-extracted to enrich for fragments between ~ 200–300 bp). e-f. Metaplots and heatmaps depicting OLDN occupancy over all genes (e) and gene-distal DHSs (f) under conditions of low (left) and high (right) MNase digestion (DHSs from GSM1014154 [37]). OLDNs were enriched by gel extraction (~ 200–300 bp) and bioinformatically filtered by fragment size (230–270 bp). n = 3 (mean).