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. 2018 Dec 1;32(23-24):1472–1484. doi: 10.1101/gad.319475.118

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© 2018 Rubio et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 4. — Control of genome-wide responses to dsDNA by m⁶A demethylase ALKBH5 and m⁶A methylase subunit METTL14. Volcano plots show differentially expressed genes (adjusted P-value < 0.01) identified from RNA-seq of polyadenylated RNA collected from cells transfected with ALKBH5 siRNA (siALKBH5; n = 3 biological replicates) (A) or METTL14 siRNA (siMETTL14; n = 3 biological replicates) (B) and stimulated with dsDNA for 12 h. Genes up-regulated versus a nonsilencing siRNA control (stimulated with dsDNA for 12 h; n = 3 biological replicates) are shown in red, while down-regulated genes are shown in blue. Nonregulated genes are shown in gray. (C) One-thousand-four-hundred-forty-seven significantly regulated genes (P < 0.01) overlap between data sets generated using siALKBH5 and siMETTL14. A scatter plot of these shows genes that are commonly up-regulated or down-regulated following either METTL14 or ALKBH5 silencing (highlighted in red and blue, respectively). Genes regulated in a reciprocal manner are highlighted in green (up-regulated when METTL14 is silenced and down-regulated when ALKBH5 is silenced) and yellow (down-regulated when METTL14 is silenced and up-regulated when ALKBH5 is silenced). The red circle highlights the IFNB1 mRNA. (D) Heat map depicting 349 ISGs, colored according to log₂ fold change in expression versus the nonsilencing siRNA control. (E,F) Pathway analyses (gene ontology direct terms) of significantly differentially expressed genes from A and B were conducted using DAVID and filtered according to a Benjamini-Hochberg procedure (<0.05).