Supplementary Figure 15: Correlation of MeCP2-dependent gene regulation with gene length and DNA methylation in neuronal nuclei.

Johnson et al. recently reported that MeCP2 mutations cause the downregulation of long gene mRNA, in neuronal nuclei, and that these long gene transcripts are subsequently up-regulated in the cytoplasm through an as yet undescribed post-transcriptional mechanism⁵⁶. However, in this study⁵⁶ the association between gene body DNA methylation and changes in gene expression was not analyzed. (a-c) Reanalysis of gene expression differences between biotin-tagged Mecp2^R106W/y excitatory neurons (mutant) and biotin-tagged WT MeCP2 excitatory neurons (WT) from Johnson et al. shows that genes with high levels of DNA methylation are preferentially up-regulated in the nuclei of male biotin-tagged Mecp2-mutant mice compared to wild-type controls. Mean fold-change of significantly regulated gene expression (FDR < 0.1, mutant versus WT) in male (A, 50 gene bins, 5 gene step) or female (b, 30 gene bins, 3 gene step) Mecp2 knockin mice binned according to the fraction of excitatory neuron DNA methylation (mCA/CA)⁵⁷. Male gene expression compares separate mutant and wild-type control mice, while the female gene expression compares mutant and wild-type cells within the same animal. (c) Mean fold-change in significantly regulated gene expression (FDR < 0.1, female mutant versus WT) for genes with high levels of DNA methylation (top 50% mCA/CA) or low levels of DNA methylation (bottom 50% mCA/CA) binned according to gene length (20 gene bins, 2 gene step). The lines represent mean fold-change in expression for genes binned as described; the ribbon is s.e.m. of each bin.