The roles of Rett Syndrome protein MECP2 at gene regulatory elements

Rett Syndrome (RTT) is a progressive neurological disorder characterized by severe cognitive and motor impairments caused primarily by mutations in MECP2. The molecular mechanisms by which disruption of MECP2 gives rise to RTT remain unclear. MECP2 is known to bind to methylated DNA in the brain, regulating the expression of neuronal genes. However, previous studies have shown complex patterns of gene dysregulation in RTT that challenge this model, such that only a subset of genes appear to be regulated by MECP2 binding to DNA methylation. We recently discovered that MECP2 preferentially binds to specific gene enhancers that we named MECP2-Binding Hotspots (MBHs). Surprisingly, MECP2 binds to these MBHs independently of DNA methylation, contrasting with its well-established role in binding methylated DNA. At MBHs, MECP2 appears to act as a repressor of enhancer activity. Importantly, over 60% of genes derepressed upon MECP2 deletion are associated with MBHs, suggesting that MBHs might be a major mechanism by which MECP2 controls genes. Preliminary analyses indicate that MBHs, but not MECP2 bound to methylated sites across the genome, are bound by histone deacetylase-containing nuclear receptor co- repressor (NCOR) complex, suggesting that MBHs may repress enhancer activity by recruiting the NCOR complex to enhancers. Taken together, our findings indicate a previously uncharacterized mechanism of transcriptional regulation by MECP2. Moreover, these results implicate dysregulation of specific enhancers as a possible mechanism underlying RTT. To gain insights into how MECP2 regulates genes and how dysregulation of MECP2 leads to RTT, we propose to (1) define the interaction between MECP2 and MBHs, and (2) elucidate the molecular mechanisms by which MBHs repress enhancers. This work has significant implications for understanding the molecular basis of MECP2 function and the complex gene dysregulation observed in RTT and will uncover new therapeutic targets and strategies for treating RTT. Project Number: 1R01MH142417-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Mental Health (NIMH) | Principal Investigator: Hume Akahori Stroud | Institution: UT SOUTHWESTERN MEDICAL CENTER, DALLAS, TX | Award Amount: $641,828 | Activity Code: R01 | Study Section: Developmental Brain Disorders Study Section[DBD] View on NIH RePORTER: https://reporter.nih.gov/project-details/11272760