Extended Data Fig. 2: High enrichment of ELL3 at L1Md_Ts.
a, RT-qPCR showing the levels of L1Md A, L1Md T, and L1Md Gf RNAs in WT and Ell3 KO mESCs. b, Pie chart showing the percentage of ELL3 peaks overlapping with a transcription start site (TSS), residing within a gene (inside), or upstream or downstream of the nearest gene. Multi-mapped reads were used for the analysis. c, Heat maps showing ELL3 ChIP-seq profile in mESCs and mappability at the ELL3 bound L1Md_Ts, L1Md_Gfs and non-REs. Shown are ± 5 kb of the center of ELL3 or TET1 peaks. d, Metaplot showing ELL3 ChIP-seq profile along L1Md_T. Mappabilty is also shown. c,d, Multi-mapped and uniquely mapped reads were used for the analysis, as indicated. e, ChIP-qPCR showing loss of the binding of ELL3 to L1Md_T after Ell3 KO. Hemo serves as a negative control for ChIP-qPCR. f, Correlation plot showing the enrichment of ELL3 at L1Md_T in the current study versus in the previous study used a different antibody. g, ChIP-seq browser tracks showing the localization of ELL3 at Akt3_L1. h, Box plots showing the length of all L1Md_Ts (n = 23,233) and the ELL3 bound L1Md_Ts (n = 1,927). Multi-mapped reads were used for the analysis. The box edges in box plots showing 25th and 75th percentiles, the center line showing the 50th percentile, and the bars showing 1.5× the interquartile range (75th percentile -25th percentile). i, MA plot showing differentially expressed genes after Ell3 KO. Significantly up- and down-regulated genes within 50 kb of the ELL3 bound L1Md_Ts are shown in red and blue, respectively. Uniquely mapped reads were used for the analysis. j, RT-qPCR showing the levels of Xlr3a and Xlr4b RNAs in WT and Ell3 KO mESCs. k, ChIP-seq browser tracks showing the localization of ELL3 at the L1Md_T located within the Xlr locus. a,e, and j, Data are the mean ± SEM from 3 independent experiments. Two-tailed unpaired Student’s t-test was performed. f,g, and k, Multi-mapped reads were used for the analysis. Source numerical data are available in source data.
