Hi-C in MGE, CGE, LGE and cortical regions from mouse embryonic forebrain

ABSTRACT: While comparative genetic analysis has been performed between distinct regions of the embryonic forebrain, a comprehensive characterization of differential epigenomic organization has not been performed. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a ‘ground truth’ epigenomic landscape at this critical stage of neurogenesis.

ORGANISM(S): Mus musculus

PROVIDER: GSE201186 | GEO | 2022/07/01

REPOSITORIES: GEO