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. 2020 Feb 28;11:1112. doi: 10.1038/s41467-020-14916-7

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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 ChIP-qPCR for OCT4, P300 and MED1 at indicated sites (arrowheads) along the Klf4-associated SE in Esrrb^−/− and control (^f/f) ESCs. Data are expressed as fold enrichment over input and normalised to a flanking control (C) region. Data are represented as means (bar plots) and individual values (dots) of independent experiments (n = 3 for OCT4 and P300; n = 4 for MED1). *Statistically significant difference (Mann–Whitney test, p < 0.05). b Top: ATAC-seq in serum/LIF (ser), MED1 in 2i/LIF (2i) and ESRRB in serum/LIF (ser) (Supplementary Data 1) along with MED1 and H3K27ac in control (ser^f/f) and Esrrb^−/− ESCs grown in serum/LIF (ser^−/−) at the Klf4 locus. Y-axis indicates RPKM and starts at 0; bottom: 4C-seq interactions between the Klf4 promoter viewpoint (blue band) and SE in control ESCs grown in 2i/LIF (2i^f/f) or in serum/LIF (ser^f/f), and in serum/LIF Esrrb^−/− ESCs (ser^−/−). Y-axis indicates RPKM and starts at 0. The bottom two tracks show the 4C-seq interaction fold changes (log2) in 2i^f/f and ser^−/− compared to ser^f/f in bins of 5 kb. Promoter–SE interactions at the ESRRB/MED1 occupied DM regions (yellow bands) are significantly stronger in 2i and weaker in ser^−/−. *p < 0.05, **p < 0.01; DEseq2; (n = 3 independent experiments). c ChIP-qPCR for POL2 at the same sites as in a in Esrrb^−/− and Esrrb^f/f ESCs. Data are expressed as fold enrichment over input and normalised to control (C) region. Data are represented as means and individual values of independent experiments (n = 4). Statistically significant difference (Mann–Whitney U test, *p < 0.05). d Expression of eRNA at the same sites as in a in Esrrb^−/− and Esrrb^f/f ESCs. Data are normalised to control (C) region and are represented as means and individual values of biological replicates; (n = 2 for Esrrb^−/−; n = 3 for Esrrb^f/f). *Statistically significant difference (Mann–Whitney test, p < 0.05). e MED1 and H3K27ac occupancy changes in Esrrb^−/− (ser^−/−) compared to control (ser^f/f) ESCs. PCC, Pearson’s correlation coefficient; (n = 2 independent experiments). f ChIP-seq tracks of MED1 and H3K27ac in Esrrb^−/− (ser^−/−) and control (ser^f/f) ESCs, as well as ESRRB and ATAC at Lefty1 and Spry4 -associated SEs. Source data are provided as Supplementary Data 10.