Figure 1. (A) The VEGF promoter PQS and scheme of G oxidation to OG, as well as (B) the proposed APE1-dependent pathway ... Figure 1. (A) The VEGF promoter.

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Figure 1. (A) The VEGF promoter PQS and scheme of G oxidation to OG, as well as (B) the proposed APE1-dependent pathway ... Figure 1. (A) The VEGF promoter PQS and scheme of G oxidation to OG, as well as (B) the proposed APE1-dependent pathway for transcriptional modulation. The previous studies from our laboratory placed the G-rich sequence between –16 to –64 relative to the transcription start site of the SV40 promoter in the coding strand, and controls conducted with a G4-negative sequence support the non-canonical structure participates in gene modulation (11,25); however, the currently available data cannot speak to the role of the i-motif fold in the process. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 Nucleic Acids Res, gkz207, https://doi.org/10.1093/nar/gkz207 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. Diagrams of the SV40 promoter to illustrate the location of functional sequences and the plasmid containing ... Figure 2. Diagrams of the SV40 promoter to illustrate the location of functional sequences and the plasmid containing the two luciferase genes studied. The black arrows depict sites where the VEGF PQS was studied in the promoter. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 Nucleic Acids Res, gkz207, https://doi.org/10.1093/nar/gkz207 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. Changes in Rluc expression observed as the VEGF PQS with no base modifications replaced key sequence elements ... Figure 3. Changes in Rluc expression observed as the VEGF PQS with no base modifications replaced key sequence elements in the SV40 promoter. (A) Promoter diagram to identify the color key for the plots. Relative response ratios (RRR = Rluc/luc) measured when the VEGF PQS replaced key elements of the SV40 promoter in plasmids that were transfected in (B) U87, (C) HepG2 or (D) HeLa cell lines. The values were normalized to the native SV40 promoter for comparison (normalized RRR = RRR<sub>expt</sub>/RRR<sub>SV40</sub>). The luciferase expression levels were determined using a dual-glo luciferase assay conducted 48 h post transfection. The RRRs measured were normalized to the native psiCHECK2 plasmid RRR in the same cell line to account for cell-specific differences in expression. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 Nucleic Acids Res, gkz207, https://doi.org/10.1093/nar/gkz207 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 4. The impact of modifying the VEGF PQS with OG or an abasic site analog F at various locations in the SV40 ... Figure 4. The impact of modifying the VEGF PQS with OG or an abasic site analog F at various locations in the SV40 promoter. Data obtained with the G-rich sequence with and without modifications were placed in the (A) coding or (B) template strand of the promoter. The VEGF PQS installed, the site of the modifications, and their chemical structures are provided in Figure 1A. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 Nucleic Acids Res, gkz207, https://doi.org/10.1093/nar/gkz207 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. Gene expression measured in U87 cells for a G4-negative sequence in the WT, OG- or F-modified states in ... Figure 5. Gene expression measured in U87 cells for a G4-negative sequence in the WT, OG- or F-modified states in plasmids at the (A) TATA box or (B) SPHII sites in the SV40 promoter. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 Nucleic Acids Res, gkz207, https://doi.org/10.1093/nar/gkz207 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 6. Distribution of (A) PQSs and (B) RNA pol II ChIP-Seq enriched peaks with PQSs flanking human TSSs on the ... Figure 6. Distribution of (A) PQSs and (B) RNA pol II ChIP-Seq enriched peaks with PQSs flanking human TSSs on the coding or template strand. Genome-wide the coding strand has 99,585 PQSs and the template strand has 94,588 PQSs flanking TSSs. Inspection of RNA pol II ChIP-Seq peaks of enrichment from U87 cells found 3,826 PQSs in the coding strand and 3,010 PQSs in the template strand. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 Nucleic Acids Res, gkz207, https://doi.org/10.1093/nar/gkz207 The content of this slide may be subject to copyright: please see the slide notes for details.