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Epigenetic and Transcriptional Dynamics of Notch Program in Intestinal Differentiation

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Intestinal Differentiated Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2650))

Abstract

The equilibrium between stem cell self-renewal and differentiation followed by proper lineage specification of progenitor cells is considered imperative for maintaining intestinal homeostasis. In the hierarchical model, intestinal differentiation is defined by the stepwise acquisition of lineage-specific mature cell features, where Notch signaling and lateral inhibition instructively regulate the cell-fate decisions. Recent studies reveal a broadly permissive intestinal chromatin underlies the lineage plasticity and adaptation to diet mediated by Notch transcriptional program. Here, we review the conventional understanding of Notch programming in intestinal differentiation and describe how new data from epigenetic and transcriptional analyses may refine or revise the current view. We provide instructions on sample preparation and data analysis and explain how to use ChIP-seq and scRNA-seq in combination of lineage tracing assay to determine the dynamics of Notch program and intestinal differentiation in the context of dietary and metabolic regulation of cell-fate decisions.

Shahadat Rahman and Xi Lan contributed equallty to this work

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Author notes

    Authors and Affiliations

    1. Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA

      Shahadat Rahman, Rayan El-Kholdi & Chia-Wei Cheng

    2. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA

      Xi Lan, Omer H. Yilmaz & Chia-Wei Cheng

    3. Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

      Christopher Terranova

    4. Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA

      Chia-Wei Cheng

    5. ESPCI Paris, Université PSL, Paris, France

      Rayan El-Kholdi

    Authors
    1. Shahadat Rahman
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    2. Xi Lan
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    3. Christopher Terranova
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    4. Rayan El-Kholdi
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    5. Omer H. Yilmaz
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    6. Chia-Wei Cheng
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    Corresponding author

    Correspondence to Chia-Wei Cheng .

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    Editors and Affiliations

    1. Biodiscovery Inst- 3, University Park, University of Nottingham, Nottingham, UK

      Paloma Ordóñez-Morán

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    © 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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    Rahman, S., Lan, X., Terranova, C., El-Kholdi, R., Yilmaz, O.H., Cheng, CW. (2023). Epigenetic and Transcriptional Dynamics of Notch Program in Intestinal Differentiation. In: Ordóñez-Morán, P. (eds) Intestinal Differentiated Cells. Methods in Molecular Biology, vol 2650. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3076-1_7

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    • DOI: https://doi.org/10.1007/978-1-0716-3076-1_7

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    • Publisher Name: Humana, New York, NY

    • Print ISBN: 978-1-0716-3075-4

    • Online ISBN: 978-1-0716-3076-1

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