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. 2015 Nov 18;17(1):79–93. doi: 10.15252/embr.201540476

Figure EV2. Paired‐end mode chromatin‐seq of abo1Δ.

Figure EV2

  1. Ethidium‐stained agarose gel separations of the two DNA pools (Biorep1 and Biorep2) extracted from MNase‐digested S. pombe chromatin and used for chromatin sequencing in this study.
  2. Frequency distributions of paired‐read end‐to‐end size values after chromatin‐seq of DNAs shown in (A). Note that increased MNase digestion used for Biorep2 samples shifts end‐to‐end size values downwards as expected.
  3. Nucleosome positions in wild‐type (Biorep1) cells were defined as the locations of 150 ± 30 bp (nucleosome) size class particle frequency peak summits (frequency value > 25). This simple heuristic procedure identifies 60,658 putative positioned nucleosomes in the S. pombe genome. The nucleosome size class particle frequency distributions centred on and surrounding (± 1,200 bp) these positions were then smoothed using an Epanechnikov kernel density estimate (to match that of a previously published data set (Gene Expression Omnibus GSE40451 30), summed and normalised to the average frequency value occurring in the ± 1,200 bp window, for each of the data sets. These cumulative distributions reveal the average nucleosome organisation surrounding positioned nucleosomes in the genome of each cell type. Three pair‐wise comparisons are shown. The nucleosome distribution from wild‐type Biorep1 overlaps with that in a previously published wild‐type data set (Gene Expression Omnibus GSE40451 30), confirming that our nucleosome mapping method yields similar results to those obtained using other technology. The abo1∆ mutant nucleosome distributions observed in Bioreps 1 and 2 both show a lower peak height and higher trough depth than the corresponding wild‐type. The wavelength of the peak pattern is shown and is equal to the known S. pombe nucleosome repeat length.
  4. Genome browser plot of wild‐type nucleosome occupancy data set (Gene Expression Omnibus GSE40451 30) plotted in relation to the 150 ± 30 bp paired‐read mid‐point frequency data obtained in this study (smoothed using an Epanechnikov kernel density estimate). Peak positions match between the two wild‐type data sets, confirming that the 150 ± 30 bp class of paired sequence reads accurately represents nucleosomal species from chromatin. Nucleosome positions in the wild‐type Biorep1 data set defined by our heuristic peak marking procedure are shown as “marked nucleosomes”.