m5C methylated lncRncr3–MeCP2 interaction restricts miR124a-initiated neurogenesis.

Coordination of neuronal differentiation with expansion of the neuroepithelial/neural progenitor cell (NEPC/NPC) pool is essential in early brain development. Our in vitro and in vivo studies identify independent and opposing roles for two neural-specific and differentially expressed non-coding RNAs derived from the same locus: the evolutionarily conserved lncRNA Rncr3 and the embedded microRNA miR124a-1. Rncr3 regulates NEPC/NPC proliferation and controls the biogenesis of miR124a, which determines neuronal differentiation. Rncr3 conserved exons 2/3 are cytosine methylated and bound by methyl-CpG binding protein MeCP2, which restricts expression of miR124a embedded in exon 4 to prevent premature neuronal differentiation, and to orchestrate proper brain growth. MeCP2 directly binds cytosine-methylated Rncr3 through previously unrecognized lysine residues and suppresses miR124a processing by recruiting PTBP1 to block access of DROSHA-DGCR8. Thus, miRNA processing is controlled by lncRNA m⁵C methylation along with the defined m⁵C epitranscriptomic RNA reader protein MeCP2 to coordinate brain development. Here, the authors identify MeCP2 as a cytosine methylated RNA reader protein that binds directly to m5C modified lncRNA lnRncr3 to maintain the neural progenitor pool and to block the processing of the embedded miR124a to limit neuronal differentiation. [ABSTRACT FROM AUTHOR]