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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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    1. David U. Gorkin & Iros Barozzi & Yuan Zhao & Yanxiao Zhang & Hui Huang & Ah Young Lee & Bin Li & Joshua Chiou & Andre Wildberg & Bo Ding & Bo Zhang & Mengchi Wang & J. Seth Strattan & Jean M. Davidson, 2020. "An atlas of dynamic chromatin landscapes in mouse fetal development," Nature, Nature, vol. 583(7818), pages 744-751, July.
    2. Yad Ghavi-Helm & Felix A. Klein & Tibor Pakozdi & Lucia Ciglar & Daan Noordermeer & Wolfgang Huber & Eileen E. M. Furlong, 2014. "Enhancer loops appear stable during development and are associated with paused polymerase," Nature, Nature, vol. 512(7512), pages 96-100, August.
    3. Ryan S. Ziffra & Chang N. Kim & Jayden M. Ross & Amy Wilfert & Tychele N. Turner & Maximilian Haeussler & Alex M. Casella & Pawel F. Przytycki & Kathleen C. Keough & David Shin & Derek Bogdanoff & Ana, 2021. "Single-cell epigenomics reveals mechanisms of human cortical development," Nature, Nature, vol. 598(7879), pages 205-213, October.
    4. Bosiljka Tasic & Zizhen Yao & Lucas T. Graybuck & Kimberly A. Smith & Thuc Nghi Nguyen & Darren Bertagnolli & Jeff Goldy & Emma Garren & Michael N. Economo & Sarada Viswanathan & Osnat Penn & Trygve B, 2018. "Shared and distinct transcriptomic cell types across neocortical areas," Nature, Nature, vol. 563(7729), pages 72-78, November.
    5. Ludo Waltman & Nees Eck, 2013. "A smart local moving algorithm for large-scale modularity-based community detection," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 86(11), pages 1-14, November.
    6. David U. Gorkin & Iros Barozzi & Yuan Zhao & Yanxiao Zhang & Hui Huang & Ah Young Lee & Bin Li & Joshua Chiou & Andre Wildberg & Bo Ding & Bo Zhang & Mengchi Wang & J. Seth Strattan & Jean M. Davidson, 2020. "Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development," Nature, Nature, vol. 586(7831), pages 31-31, October.
    7. Rongxin Fang & Sebastian Preissl & Yang Li & Xiaomeng Hou & Jacinta Lucero & Xinxin Wang & Amir Motamedi & Andrew K. Shiau & Xinzhu Zhou & Fangming Xie & Eran A. Mukamel & Kai Zhang & Yanxiao Zhang & , 2021. "Comprehensive analysis of single cell ATAC-seq data with SnapATAC," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    8. Christian Mayer & Christoph Hafemeister & Rachel C. Bandler & Robert Machold & Renata Batista Brito & Xavier Jaglin & Kathryn Allaway & Andrew Butler & Gord Fishell & Rahul Satija, 2018. "Developmental diversification of cortical inhibitory interneurons," Nature, Nature, vol. 555(7697), pages 457-462, March.
    9. Kathryn C. Allaway & Mariano I. Gabitto & Orly Wapinski & Giuseppe Saldi & Chen-Yu Wang & Rachel C. Bandler & Sherry Jingjing Wu & Richard Bonneau & Gord Fishell, 2021. "Genetic and epigenetic coordination of cortical interneuron development," Nature, Nature, vol. 597(7878), pages 693-697, September.
    10. Junyue Cao & Malte Spielmann & Xiaojie Qiu & Xingfan Huang & Daniel M. Ibrahim & Andrew J. Hill & Fan Zhang & Stefan Mundlos & Lena Christiansen & Frank J. Steemers & Cole Trapnell & Jay Shendure, 2019. "The single-cell transcriptional landscape of mammalian organogenesis," Nature, Nature, vol. 566(7745), pages 496-502, February.
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