Supplemental Material for Cole and Dennis, 2020

Figure S1. Specific enrichment of MNase-seq fragments at promoters using mTSS-Seq, related to all figures.

(A) Average plots of sequence-captured GM12878 MNase-seq replicates across the TSS +/- 1000bp, all fragments.

(B) Histogram of fragment sizes for GM12878 heavy and light MNase digests

(C) Schematic demonstrating targeted enrichment with hg19 SeqCap oligos (mTSS-seq). GM12878 Untreated data for chromosome 20 shown in the UCSC genome browser (genome.ucsc.edu), with multiple magnifications down to a single TSS, CD40, compared to a previously published nucleosome mapping data set from Gaffney et al., 2012.

Figure S2. Total nucleosome occupancy of replicate untreated GM12878 cells, related to all Figures.

Total nucleosome occupancy was determined for all human promoters centered on the TSS (+/-1kb). Rep 1 and Rep 2 untreated control samples were sorted into quartiles based on maximum signal.

Figure S3. Sort of nucleosome occupancy changes dependent on gene expression in GM12878 cells, related to Figure 2.

The log₂ratio of the total nucleosome occupancy of 20 minute HKST-treated cells/untreated control cells was sorted into quartiles based on total gene expression (GSM2344230).

Figure S4. Independent sorts of MNase-sensitivity of untreated and 20 minute HKST GM12878 cells, related to Figure 2.

(A) The log₂ratio of light/heavy MNase digest (MNase sensitivity) was determined for all human promoters centered on the TSS (+/-1kb). The MNase sensitivity for the untreated control cells was sorted with k-means clustering (k=7) and the MNase-sensitivity data for 20 minute post-HKST treatment was sorted independently with k-means clustering (k=7). Average sensitivity profiles per cluster are shown below the heatmaps for each time point.

(B) Venn diagram representing the unique and shared promoters that are present in the independent sorts of the untreated and 20 minute post-HKST samples.

Figure S5. Independent sorts of maximum MNase-sensitivity of untreated, 20 minute, 40 minute, and 60 minute HKST GM12878 cells, related to Figure 3.

The log₂ratio of light/heavy MNase digest (MNase sensitivity) was determined for all human promoters centered on the TSS (+/-1kb). The MNase sensitivity for all experimental conditions was sorted into quartiles independently based on maximum sensitivity. Average sensitivity profiles per cluster are shown below the heatmaps for each time point.

Table S1. Results of the gene ontology analysis and gene lists for the 20 minute post-HKST -1 sensitive nucleosome cluster, related to Figure S4.

Table S2. Results of the gene ontology analysis and gene lists for the untreated control -1 sensitive nucleosome cluster, related to Figure S4