Identification of conserved cis-regulatory elements impact Mecp2 level and neurological functions
Methyl-CpG binding protein 2 (MeCP2) is a nuclear protein that binds to methylated cytosines and regulates gene expression. Normal brain function requires precise control of MeCP2 level. Loss of function mutations in the X-linked gene, MECP2 cause Rett Syndrome (RTT), a progressive neurological disorder. Increase in MeCP2 level leads to the neurological disorder MECP2 duplication syndrome (MDS). Despite the functional importance of MeCP2 in the brain, its transcriptional regulation remains poorly understood. Here, we utilized ATAC-seq in the mouse brain across development to identify five putative adult brain cis-regulatory elements (CREs) of Mecp2. We found that knocking out these CREs using CRISPR-Cas9 altered Mecp2 levels. Furthermore, two of the CREs were conserved in human, and when we delete either of these in mice, the animals show progressive neurological dysfunction. Deletion of one of the conserved CREs led to a decreased MeCP2 level and caused phenotypes similar, albeit milder, to those seen in Mecp2-null mice whereas the deletion of the second CRE led to an increased MeCP2 level and phenotypically resembled, but also milder than, MECP2 duplication mice. Deleting these two conserved CREs levels in human iPSC-derived neurons also similarly altered MECP2 levels. Taken together, our discovery of CREs that modulate Mecp2/MECP2 expression provides insight into regulation of Mecp2/MECP2 in the mouse brain and human neurons, respectively. These CREs could be candidate sites for non-coding mutations that lead to neurodevelopmental disorders characterized by partial features of RTT or MDS. Overall design: Nuclei were isolated from adult wildtype liver and brain, P6 brain and embryonic day 12 brain for ATAC-Sequencing.