Extended Data Fig. 4: The ELL3 regulated L1Md_T 5’UTRs are marked by H3K27ac in naïve mESCs.
a, RNA-seq browser tracks showing RNA levels of Rpl7 and Rpl3 after Ell3 KO or LINE-1 ASO treatment in mESCs. Uniquely mapped reads were used for the analysis. b, RT-qPCR showing that L1Md_A and L1Md_Gf remain unchanged after Akt3_L1 CRISPRa. c, Heat maps showing H3K27ac profiles at the ELL3 bound L1Md_T, L1Md_Gf, and non-RE regions, and the ELL3 free but TET1 bound L1Md_A regions in naïve or primed mouse ESCs, and different stages of embryos and indicated tissues. d, ChIP-seq browser tracks showing increased H3K27ac levels, and hMeDIP-seq browser tracks showing reduced 5hmC levels after Ell3 KO at the L1Md_T near to Lipo3, or within Sema3c. Multi-mapped reads were used for the analyses. Virtual 4 C analyses showing that the promoters of Lipo3and Aldh1a2 are able to physically interact with their nearby L1Md_Ts, respectively. e, Browser tracks showing that the L1Md_Ts within Drp2 and Mast2 are not bound by ELL3, and that physical interaction between the L1Md_Ts within these two genes and their promoters are not observed. d,e, Blue bars indicating the view points, and orange bars indicating the putative enhancer regions. Multi-mapped reads were used for the analysis unless otherwise indicated. f, Diagram illustrating the positions of the primers used to amplify the regions in the vicinity of the Akt3 promoter. g, qPCR showing that neither downstream nor upstream region of the Akt3 promoter is enriched in the HA ChIP in the Akt3_L1 CRISPRa cells. b, and g, Data are the mean ± SEM from 3 independent experiments. Two-tailed unpaired Student’s t-test was performed. Source numerical data are available in source data.
