Fig. 3: The selective MYC-G4 ligand DC-34 matches ATENA. | Nature Communications

Fig. 3: The selective MYC-G4 ligand DC-34 matches ATENA.

From: Chemically modified CRISPR-Cas9 enables targeting of individual G-quadruplex and i-motif structures, revealing ligand-dependent transcriptional perturbation

Fig. 3: The selective MYC-G4 ligand DC-34 matches ATENA.The alternative text for this image may have been generated using AI.

a Chemical structure of DC-34. b RT-qPCR for c-MYC expression in MCF7 cells treated with increasing concentrations of DC-34 for 48 h. Values are represented as fold change (\({2}^{-\triangle \triangle {C}_{t}}\)) with respect to the mock (DMSO-treated) and normalized for the housekeeping gene GAPDH. Mean ± SD, n = 3, biological replicates, each of which included two technical replicates. c RT-qPCR for P1-driven c-MYC expression in MCF7 cells treated with different concentrations of DC-34 for 48 h. Values are represented as fold change (\({2}^{-\triangle \triangle {C}_{t}}\)) with respect to the mock (DMSO-treated) and normalized for the housekeeping gene GAPDH. Mean ± SD, n = 3, biological replicates, each of which included two technical replicates. d Evaluation of potential DC-34 off-targets by analyzing the KRAS expression using the same samples reported in (c). e BG4 CUT&Tag-qPCR for MCF7 cells treated with DMSO (mock) or (7.5 µM) DC-34. BG4 accessibility was analyzed for c-MYC and normalized to three G4s in control gene sites (RPA3, MAZ, RBBP4). n = 2, biological replicates, including three technical replicates for BG4 and one for the negative (no BG4 treatment). f Volcano plot of DEGs in MCF7 cells treated with DC-34 vs cells treated with DMSO (mock). Gray = non-significant genes (FDR ≥ 0.05 or |log₂FC| <1); red = upregulated DEGs (FDR < 0.05, log₂FC ≥ +1); blue = downregulated DEGs (FDR < 0.05, log₂FC ≤ −1). g Volcano plot of DEGs in MCF7 cells transfected with sgRNAMYC-19 treated with Cl-PyPDS2 vs mock, after sgRNA NTC filtering; Red = upregulated DEGs (FDR < 0.05, log₂FC ≥ +1); blue = downregulated DEGs (FDR < 0.05, log₂FC ≤ −1). Plot includes only genes passing FDR < 0.05 and |log₂FC | ≥ 1. The data presented are the mean of n = number of independent biological samples. Statistical significance was calculated using a Welch-corrected two-tailed t test in GraphPad Prism; p-value: ns > 0.05, *≤0.05, **≤0.01, ***≤0.001, ****≤0.0001. Source data are provided as a Source Data file.

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