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. 2020 Jul 25;48(16):8993–9006. doi: 10.1093/nar/gkaa613

Figure 5.

Figure 5.

DSBs anti-correlates with nucleosome occupancy in human MCF-7 cells. (A) Interrogation of public datasets: The probability of harboring endogenous DSBs anticorrelates with nucleosome occupancy. This hypothesis was tested on BLISS and ATAC datasets produced and published by other groups: ATAC-seq GSE101736, GSM2714245; BLISS GSE136365, GSM4047452 (left) and GSM4047456 (right). Each dot represents one percentile in nucleosome occupancy. The x-axis, log scale, is the nucleosome occupancy value; the y-axis, log scale, is the probability to harbor one or more DSBs. Statistics: Pearson correlation on the log-transformed values. (B) Estimated number of DSBs in MCF-7 cells, expressed as fold change over the paired control sample (not treated not irradiated). MCF-7 cells were pre-treated (magenta) or not (green) with 10 mM N-acetyl-l-cysteine (NAC) for 1 h and irradiated or not with 10 Gy; dots and lines represent biological replicates and averages, respectively. Statistics: two-way ANOVA test (paired experiments). Irradiation dose (P = 0.0063) and interaction of irradiation and NAC treatment (P = 0.043) are statistically significant; NAC treatment (P = 0.28) is not. (C) The probability of harboring DSBs anticorrelates with nucleosome occupancy. Each dot represents one percentile in nucleosome occupancy (ATAC-seq raw data from GSE101736). The x-axis, log scale, is the nucleosome occupancy value; the y-axis, log scale, is the probability to harbor one or more DSBs. Statistics: Pearson correlation on the log-transformed values.