MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (FP PRO-Seq)

Mutations in the methyl-DNA-binding repressor protein MeCP2 cause the devastating neurodevelopmental disorder Rett syndrome. It has been challenging to understand how MeCP2 regulates transcription because MeCP2 binds broadly across the genome, and MeCP2 mutations are associated with widespread small-magnitude changes in neuronal gene expression. Using multiple approaches, we demonstrate that MeCP2 represses nascent RNA transcription of highly methylated long genes in the brain through its interaction with the NCoR co-repressor complex. By measuring the rates of transcriptional initiation and elongation in the brain directly, we find that MeCP2 has no measurable effect on transcriptional elongation, but instead represses the rate at which Pol II initiates transcription of highly methylated long genes. These findings suggest a new model of MeCP2 function in which it binds broadly across highly methylated regions of DNA, but acts from a distance to attenuate transcriptional initiation. Overall design: Flavopiridol (FP) was injected for 0, 20, 40, or 60 minutes into MeCP2 KO or WT mice (n = 2 or 3), followed by nuclei isolation from forebrain tissue and Precision Run-On sequencing (PRO-seq) to measure rates of transcriptional elongation and initiation.