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. 2021 Mar 1;49(6):3217–3241. doi: 10.1093/nar/gkab099

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© The Author(s) 2021. 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-NonCommercial 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 5. — Regulated genes and their association with BZLF1 ChIP-seq peaks and binding motifs in promoter regions. (A, E) The numbers of ChIP-seq defined peaks are plotted on the x-axis versus the magnitude of gene regulation expressed as ‘log₂ fold change’ on the y-axis after doxycycline induced expression of full-length BZLF1 in Raji iBZLF1 (A) and DG75 iBZLF1 cells (E) for 6 h. Among the regulated genes that did not encompass BZLF1 peaks within their defined promoter regions 41 and 52 genes were found up-regulated (45 resp. 48 % of all up-regulated genes) and about 4,500 and 63 genes were down-regulated (63 resp. 68 % of all down-regulated genes) in Raji and DG75 iBZLF1 cells, respectively, as indicated by the dashed horizontal green lines. Among the regulated genes with BZLF1 peaks in their promoter regions, 50 and 57 were found up-regulated (55 resp. 52 % of all up-regulated genes) and about 2.600 and 30 genes were down-regulated (37 resp. 32 % of all down-regulated genes) in Raji and DG75 iBZLF1 cells, respectively. (B, F) The number of BZLF1 motifs as defined in Figure 1C and Supplementary Figure S2 (panels C, G and K) are plotted on the x-axis versus the magnitude of gene regulation on the y-axis as in panel A. BZLF1 motifs downstream and upstream of TSSs entered the analysis. The distribution of regulated genes (y-axis) with or without BZLF1 binding sites follows the scheme in panel A. (C). The peak analysis includes the promoter proximal region −5 kb/+1 kb of the transcriptional start sites (TSS) as indicated. (D) The cartoon schematically depicts two single peaks upstream and downstream of a TSS with three and one BZLF1 motifs, respectively, illustrating the basics of this analysis and the principal location of the BZLF1 motifs.