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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE296925 | GEO | 2026/07/23

REPOSITORIES: GEO

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

Project description: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.

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Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating reelin and ciliary gene regulatory networks (snRNAseq)

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eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

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Project description:The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNA (ncRNA) transcripts in mammalian cells, bidirectional ncRNAs referred to as eRNAs are present on enhancers. However, it has remained unclear whether these eRNAs are functional, or merely a reflection of enhancer activation. Here, we report that 17 ?-estradiol (E2)-bound estrogen receptor alpha (ER?) on enhancers causes a global increase in eRNA transcription on enhancers adjacent to E2 upregulated coding genes. These induced eRNAs, as functional transcripts, appear to exert important roles for the observed ligand-dependent induction of target coding genes, causing an increased strength of specific enhancer:promoter looping initiated by ER? binding. Cohesin, present on many ER?-regulated enhancers even prior to ligand treatment, apparently contributes to E2-dependent gene activation by stabilizing E2/ER?/eRNA-induced enhancer:promoter looping. Our data indicate that eRNAs are likely to exert important functions in many regulated programs of gene transcription. The ChIP-seqs in this study measure the binding landscape of master transcription regulator of estrogen signaling - ER?, together with common histone marks including H3K27ac and H3K4me1 in MCF7 cells. These data serve as the basis to understand the enhancer map and subsequent analysis of eRNA expression using GRO-seq. The GRO-seq measures the trancription of nascent RNAs in the genome. From MCF7 cells treated with veichle or estrodial, we could identify estrogen-regulated eRNAs and subsequently could study their functions.

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