Fig. 3: Knockdown of chromatin-associated L1 RNAs influences the signature of H3K27me3 histone mark.
From: LINE-1 regulates cortical development by acting as long non-coding RNAs
a, b Inference of transcriptional/chromatin regulators in E14.5 mouse cortex electroporated with shL1-a (a) and cortical cells infected with shL1-a/b (b). The top regulators are in green for the down-regulated gene set and in brown for the up-regulated gene set. Top regulators in common between gene sets are in orange. p values were determined by gprofiler2 using a default hypergeometric test and correction for multiple testing has been performed by the g:SCS algorithm. c Cytosolic, nucleoplasmic and chromatinic abundance of L1 transcripts in 21 div cells. RNA levels are expressed as percentage of total RNA. Data are mean ± s.e.m. n = 3 independent biological replicates. d Expression of L1 transcripts in cytoplasmic, nucleoplasmic and chromatinic fractions of 21 div cells non infected (n.i.) or infected with shCtrl, shL1-a and shL1-b. RNA levels are normalized on the n.i. group for each fraction. Data are mean ± s.e.m. n = 6 independent biological samples. One-way ANOVA with Tukey’s multiple comparison test. e Metagene plot showing H3K27me3, GFP and input ChIP-seq signals for down-regulated, unchanged and up-regulated genes in mouse cortical cells infected with shCtrl or shL1-a. The plot shows the average signals of n = 2 independent biological replicates for each condition with 95% intervals of confidence as shaded areas. f Volcano plots representing differentially enriched ChIP-seq peaks in shL1-a cortical cells for H3K27me3. X-axis shows the log2 (Fold Change). The Y-axis shows the -log10 (FDR). n = 2 independent biological replicates. g Top GO terms under the biological process category for genes down-regulated by shL1s according to RNA-seq and contained in peaks/islands with a significantly higher deposition of H3K27me3 after shL1-a. p values were determined by gprofiler2 using a default hypergeometric test and correction for multiple testing has been performed by the g:SCS algorithm. Source data are provided as a Source Data file.
