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. 2020 Jun 10;6(24):eaba0777. doi: 10.1126/sciadv.aba0777

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Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

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Fig. 3 — (A) PCA of RNA-seq signals in cells transfected with OSKM and Flag, RNaseH1, or RNaseH1^D209N during reprogramming. (B) MA plots showing the DEGs (red dots) of RNaseH1^D209N/Flag and RNaseH1/Flag during reprogramming. (C) Statistics of up- or down-regulated differential R-loop regions (DRRs) of RNaseH1^D209N compared with Flag during reprogramming. (D) Scatterplots of gene expression and R-loop log₂ fold change (RNaseH1^D209N/Flag, D7). (E) Scatterplots of RNA (x axis, D7) and promoter, gene body, or terminator R-loop (y axis, D1, D3, D7) of RNaseH1^D209N compared with controls on concurrently changed genes. (F) Counts of Prom-/Gb-/Term-concurrently changed genes shown in (E) on D1, D3, and D7 during reprogramming. (G) Snapshots of ATAC-seq of MEFs reprogrammed with OSKM plus Flag and RNaseH1^D209N on day 7 at representative genomic loci. (H) Colocalization analysis of total ATAC peaks (RNaseH1^D209N + Flag, D7) and up- or down-regulated differential R-loop regions (RNaseH1^D209N/Flag, D7) in promoter, gene body, terminator, and intergenic regions.