The Sox2 Regulatory Region 42 (SRR42) Produces eRNAs that Influence Neuronal Migration during Cortical Development

During mammalian neural development, precise regulation of gene expression in neural progenitor cells (NPCs) is critical for proper formation of the cortex. Although the regulatory mechanism of the transcription factor Sox2 has been extensively examined, the role of its distal regulatory elements remains poorly understood. Here, we identified a Sox2 regulatory region located 42 kb downstream of the Sox2 TSS (SRR42) that exhibits hallmark features of an active regulatory element, including open chromatin, histone modifications, and bidirectional transcription of enhancer RNAs (eRNAs).  Using transgenic reporter mice, we found that SRR42 is specifically active in NPCs in the developing mouse brain. CRISPR-Cas9-mediated deletion of SRR42 in mice together with single-cell multiome analysis further revealed the involvement of SRR42 regions in the regulation of neuronal migration and cortical lamination. Knockdown of SRR42 eRNAs in vivo impaired neuronal migration, indicating that these eRNAs regulate neuronal development. Our study demonstrated that SRR42 functions through an eRNA-mediated mechanism to precisely control neuronal positioning during mammalian cortical development, which is not associated with Sox2 transactivation. These findings provide new insights into the epigenetic regulation of cortical formation and may help understand neurodevelopmental disorders.