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. Author manuscript; available in PMC: 2020 Sep 5.
Published in final edited form as: Mol Cell. 2019 Aug 15;75(5):905–920.e6. doi: 10.1016/j.molcel.2019.06.045

Figure 5. DNA methylation decreases MED1 association at SE, enhancer-promoter H3K27ac, and in-cis transcription of the target genes.

Figure 5.

(A) Averaged DNA FISH (Magenta, Mir290 SE) and co-immuno-fluorescence staining (Green, MED1) signal in the nuclei of MIR290-SE-TG cells sorted based on allelic methylation states. Random spots were selected in the same image away from the DNA FISH spots. (B) Peak calling from H3K27ac ChIP-seq of 4 sorted populations from MIR290-SE-TG. Mir290 SE and Mir290–295 cluster are boxed in blue. (C) Peak calling from H3K27ac ChIP-seq of 4 sorted populations from SOX2-SE-TG. Sox2 SE and Sox2 gene are boxed in blue. (D) Allele-specific expression of Mir290–295 pri-miRNA (top) and Sox2 mRNA (bottom) in 3 sorted populations, with VIC-TaqMan probe detecting the 129SE-RGM-tdTomato allele, and FAM-TaqMan probe detecting the CASTSE-RGM-eGFP allele in both SE cases. Independently targeted clones for each SE were used as biological replica. Data are represented as mean ± SD. (E) Fold-change of total Mir290–295 pri-miRNA (left) and total Sox2 mRNA (right) from the 4 sorted populations normalized to that of the T+G− population. Independently targeted clones for each SE were used as biological replica. Data are represented as mean ± SD. (F) Quantification of Mir290–295 expression on sorted SOX2-SE-TG cells compare to Sox2 expression (left), and quantification of Sox2 expression on sorted MIR290-SE-TG cells compare to Mir290–295 expression (right). Data are represented as mean ± SD. See also Figure S5.