Fig. 4

L1 promoter methylation levels and CNVs are dynamic in mouse hippocampus and cortex development. a Schematic drawing representing sagittal sections of mouse brain at different stages of embryonic-perinatal (E15.5, E18.5, P0) and postnatal (P3, P14) development. The micro-dissected regions (hippocampus, cerebral cortex, and cerebellum) are highlighted in different colors. b Schematic representation of mouse (Mm) LINE-1 (L1) Tf subfamily (L1MdTf): 5′ untranslated region (5’UTR), monomeric repeats (grey triangles), open reading frame 1 (ORF1), and open reading frame 2 (ORF2) (ORF2 includes endonuclease (EN), reverse transcriptase (RT), and cysteine-rich domains (C)), poly (A) tract (An). Within the L1 5′UTR monomer are highlighted: CpG island (CpG 1–13) and YY1 binding site (red), as reported in [37]. c Heat-map showing methylation levels of L1MdTf promoter in blood, hippocampus, cortex, and cerebellum at different stages of embryonic (E15.5, E18.5) and postnatal development (P0, P3, P14). For each organ and developmental stage, samples from 4 different embryos/mice were analyzed. For blood P0 (n = 3) (see the “Methods” section). On an average, 80,000 reads were analyzed for each sample. d Matched L1MdTf methylation and L1 CNV analysis in hippocampus, cortex, and cerebellum at different stages of embryonic (E15.5, E18.5) and postnatal development (P0, P3, P14). Upper panels: methylation analysis of L1MdTf promoter at YY1 binding site in the hippocampus, cortex, and cerebellum at different stages of embryonic (E15.5, E18.5) and postnatal development (P0, P3, P14). On an average, 80,000 reads were analyzed for each sample. Hippocampus: E15.5 vs P14, p = 0.003; E18.5 vs P0, p = 0.047; E18.5 vs P3, p = 0.009; E18.5 vs P14, p = 0.000; P0 vs P14; p = 0.027. Cortex: E15.5 vs P14, p = 0.003; E18.5 vs P3, p = 0.031; E18.5 vs P14, p = 0.000; P0 vs P14, p = 0.001; P3 vs P14, p = 0.017, ANOVA with Tukey’s post hoc test. Data are represented as the mean percentage of methylation ± S.E.M. Lower panels: L1 CNV assay performed on mouse hippocampus, cortex, and cerebellum at different stages of embryonic (E15.5, E18.5) and postnatal development (P0, P3, P14), obtained from the same 4 mice above. mL1-ORF2 was normalized on m5S. Hippocampus: E15.5 vs P3, p = 0.006; E15.5 vs P14, p = 0.000; E18.5 vs P3, p = 0.012; E18.5 vs P14, p = 0.000; P0 vs P14, p = 0.004. Cortex: E15.5 vs P3, p = 0.018; E15.5 vs P14, p = 0.000; E18.5 vs P3, p = 0.047; E18.5 vs P14, p = 0.000; P0 vs P14, p = 0.000; P3 vs P14, p = 0.005, ANOVA with Tukey’s post hoc test. Data are represented as mean ± S.E.M