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. 2020 Oct 8;11:5061. doi: 10.1038/s41467-020-18900-z

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a, b List of proteins identified by MS a and western blotting with indicated antibodies b following immunoprecipitation with anti-FLAG beads in nuclear extracts from OSKM-reprogrammed P2 MEFs with FLAG-tagged JMJD3 or UTX. RING1B is the negative control. c Immunoprecipitation with NIPBL antibody in nuclear extracts from OSKM-reprogrammed P2 MEFs with FLAG-tagged JMJD3, followed by western blotting with the indicated antibodies. d ChIP-qPCR for NIPBL at the enhancer/TSS of the indicated genes in OSKM-reprogrammed P2 MEFs with Empty or JMJD3. e Number of GFP⁺ colonies in OSKM-reprogrammed P2 MEFs with Empty or JMJD3 plus shLuc or shNipbl. f Number of GFP⁺ colonies in OG2 EpiSCs transduced with KLF4 and Empty or JMJD3 plus shLuc or shNipbl. g Violin plots of H3K27ac levels in OSKM-reprogrammed P2 MEFs with Empty or JMJD3 at TSS/enhancers of PSC-enriched genes upregulated upon JMJD3 OE at day 5 or only at day 10. h Correlation of H3K27me3 and H3K27ac changes at KLF4-binding sites by JMJD3 OE in OSKM-reprogrammed P2 MEFs with Empty or JMJD3 in medium with Vc at day 5, shown as a 2D density histogram where each point represents a KLF4-binding site. i Schematic (left panels) and 3C-PCR (right panels) of enhancer–promoter looping between the indicated sites. Arrows under restriction enzyme sites mark the orientation of the primers. j ChIP-qPCR for H3K27me3 and Pol II at the indicated loci of Sall4 in OSKM-reprogrammed P2 MEFs with Empty or JMJD3. Error bars represent the s.e.m. Data are presented as mean ± s.e.m. from n = 3 d–f, j biologically independent experiments. Statistical analyses were performed using a two-tailed unpaired Student’s t-test d, j or one-way ANOVA followed by a Dunnett multiple comparison test e, f (*P < 0.05; **P < 0.01; ***P < 0.001). P values: 0.0343, 0.0059, 0.0059, 0.0228, 0.0001, 0.0062, 0.0019 d; 0.0049, 0.0053, 0.0009, 0.0010 e; 0.0004, 0.0007, 0.0001, 0.0001 f; 0.0054, 0.0193, 0.0364, 0.0161 (H3K27me3), 0.0419, 0.0288, 0.0074, 0.0063 (Pol II) j. Experiments were repeated independently three times b or twice c, j with similar results. Source data are provided as a Source Data file.