Fig. 2

OLDN occupancy qualitatively correlates with transcription, mononucleosome occupancy, and RNAPII binding. (a) Mononucleosomes and OLDNs from HeLa cells (DRP003456 [21]), sorted by mononucleosome occupancy and visualized over hg38 RefSeq Select mRNA TSSs. Mononucleosome libraries were not gel-extracted and size-selected for fragments between 135–165 bp. OLDN libraries were gel-extracted and size-selected for fragments between 230–270 bp. n = 2. (b) As in panel a, but using mouse MNase-seq data (GSE183278 [36]) and visualized over mm10 RefSeq Select mRNA TSSs. Libraries were not gel-extracted but were bioinformatically size-selected for fragments between 135–165 bp (mononucleosomes) and 230–270 bp (OLDNs). n = 2. (c) Putative OLDNs identified from our EGFP KD (control) MNase-seq experiments visualized over TSSs (left) and gene-distal DHSs (right), sorted by mononucleosome occupancy. n = 3 merged replicates, shown as a single heatmap per condition. Gel-extracted libraries were used for these analyses and size-selected for fragments between 230–270 bp. (d) As in panel c, but sorted by nascent transcription (TT-seq data from GSE181624 [38]). Gel-extracted libraries were used for these analyses and size-selected for fragments between 230–270 bp.