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An epigenome atlas of neural progenitors within the embryonic mouse forebrain

Author

Listed:
  • 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)
    National Institutes of Health (NIH))

  • Dongjin R. Lee

    (National Institutes of Health (NIH))

  • Daniel J. Lee

    (National Institutes of Health (NIH)
    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)
    NIH)

  • Timothy J. Petros

    (National Institutes of Health (NIH))

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.

Suggested Citation

  • Christopher T. Rhodes & Joyce J. Thompson & Apratim Mitra & Dhanya Asokumar & Dongjin R. Lee & Daniel J. Lee & Yajun Zhang & Eva Jason & Ryan K. Dale & Pedro P. Rocha & Timothy J. Petros, 2022. "An epigenome atlas of neural progenitors within the embryonic mouse forebrain," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31793-4
    DOI: 10.1038/s41467-022-31793-4
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