Fig. 4

Temperature effects on DNA accessibility in nuclear chromatin of S2R+ cells. (A) Culture aliquots were shifted to the indicated temperatures and 24 h later analyzed by ATAC-Seq involving tagmentation in crude nuclei always at 25 °C. Three biological replicates were analyzed. (B) Volcano plots illustrate fold changes of read counts in ATAC-Seq peaks when comparing 14 with 29 °C. Peaks with insignificant change (FDR ≥ 0.05) are shown in grey, those with significant but limited change (FC ≤ 2) in black, and those with a strong change (FC > 2) in either blue (CoolOpen) or red (WarmOpen). (C) CoolOpen and WarmOpen regions (see panel B) have intermediate accessibility at 25 °C on average. (D) Browser tracks display read counts obtained by ATAC-Seq at the indicated temperatures within selected genome regions. While the region shown in the top panel does not include temperature-regulated genes (including sqh), the region shown in middle panel contains small Hsp genes with transcript levels that were most strongly CoolDown. The bottom panel includes betaTub97EF with strongly CoolUp transcript levels [53]. Just upstream of this betaTub97EF gene, a CoolOpen region was apparent (dashed red rectangle). In contrast, at most modest accessibility alterations appear to be induced by temperature change in the other regions