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. 2020 Feb 27;48(8):4147–4160. doi: 10.1093/nar/gkaa122

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© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — dBigH1 down-regulates gene expression. (A) Volcano plot showing the change in expression of each individual gene in cells expressing dBigH1 in comparison to control mock-induced cells. Differentially down-regulated and up-regulated genes (|FC| > 1.5; Benjamini-Hochberg adjusted P-value < 0.1) are indicated in blue and red, respectively. (B) The normalized gene expression (log₂RMA) in dBigH1-expressing cells and control mock-induced cells is presented for all genes classified according to their absolute fold-change (|FC|) expression upon dBigH1 expression. (C) Correlation of gene level dBigH1 content (log₂RPKM IP/input) and expression FC upon dBigH1 expression (log₂FC). Genes differentially up-regulated (red) and down-regulated (blue) are indicated. Non-DE genes are also indicated (light blue). Black lines are lowess regression fits for up-regulated and down-regulated genes; the average slopes (α_mean) are indicated. (D) The fold change expression with respect to control mock-induced cells of six randomly selected down-regulated genes (left) and four randomly selected up-regulated genes (right) was determined by RT-qPCR in dBigH1-expressing cells (white) (N = 7; error bars are SD; two-tailed t-test, P-values are indicated). (E) The relative GFP mRNA/DNA ratios of a chromatin template carrying a GFP-reporter gene assembled in vitro in full (white), mock-depleted (light grey) and dBigH1-depleted DREX in the absence (black) and presence of increasing amounts of bacterially-expressed dBigH1 added during assembly (dark grey) (N = 3; error bars are SD; two-tailed t-test, P-values are indicated). (F) The expression (log₂RMA) in control cells is presented for up-regulated and down-regulated genes (Wilcoxon rank sum test, P-value is indicated). (G) The pausing index of total RNApol II (Rpb3) in control cells is presented for down-regulated, non-DE and up-regulated genes (Wilcoxon rank sum test, P-values are indicated).