(A) Boxplots showing gene expression fold changes upon Fto KO from caRNA sequencing. Genes were categorized according to their genomic distance to the nearest LINE1 RNA with at least 10 reads. P value was determined using Wilcoxon rank sum test. (B) Scatter plot showing the negative correlation of fold changes between expression of LINE1-containing genes and m6A level of corresponding intragenic LINE1 RNA upon Fto KO. Intragenic LINE1 RNAs were categorized into 100 bins on the basis of their ranked expression fold changes upon Fto KO. r refers to Pearson’s correlation coefficient. P value was calculated based on t distribution. (C) Boxplots showing fold changes of gene expression from caRNA sequencing (left) and gene transcription rate (right) upon Fto KO. Genes were categorized into three groups: genes containing down-regulated LINE1 RNA, genes near (<1 Mb) down-regulated LINE1 RNA, and genes containing other LINE1 RNA. P values were determined using Wilcoxon rank sum tests. (D) Profiles of H3K4me3, H3K9me3, H3K27ac, and Pol II levels on loci of genes containing down-regulated LINE RNA from 3.0 kb upstream of the TSS and 3.0 kb downstream of the TES in WT and Fto−/− mESCs.