An epigenome atlas of neural progenitors within the embryonic mouse forebrain

Christopher T. Rhodes, Joyce J. Thompson, Apratim Mitra, Dhanya Asokumar, Dongjin R. Lee, Daniel Lee, Yajun Zhang, Eva Jason, Ryan K. Dale, Pedro P. Rocha and Timothy J. Petros ()
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Christopher T. Rhodes: National Institutes of Health (NIH)
Joyce J. Thompson: National Institutes of Health (NIH)
Apratim Mitra: National Institutes of Health (NIH)
Dhanya Asokumar: National Institutes of Health (NIH)
Dongjin R. Lee: National Institutes of Health (NIH)
Yajun Zhang: National Institutes of Health (NIH)
Eva Jason: National Institutes of Health (NIH)
Ryan K. Dale: National Institutes of Health (NIH)
Pedro P. Rocha: National Institutes of Health (NIH)
Timothy J. Petros: National Institutes of Health (NIH)

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract A comprehensive characterization of epigenomic organization in the embryonic mouse forebrain will enhance our understanding of neurodevelopment and provide insight into mechanisms of neurological disease. Here 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 with associated 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.

Date: 2022
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DOI: 10.1038/s41467-022-31793-4

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