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Chromatin Profiling of Human Naïve Pluripotent Stem Cells

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Human Naïve Pluripotent Stem Cells


Chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-sequencing) facilitates the genome-wide mapping of DNA sequences that are enriched for specific chromatin-binding proteins or histone post-translational modifications. More recently developed chromatin profiling methods called Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and Cleavage Under Targets and Tagmentation (CUT&Tag) have adapted the ChIP-sequencing approach to produce similar data from a smaller amount of starting material, and while overcoming many of the conventional drawbacks of ChIP-sequencing. Here, we present detailed protocols for ChIP-seq, CUT&RUN, and CUT&Tag to profile genome-wide protein-DNA interactions in naïve human pluripotent stem cells.

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  1. Euskirchen GM et al (2007) Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 17:898–909

    Article  CAS  Google Scholar 

  2. Robertson G et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651–657

    Article  CAS  Google Scholar 

  3. Barski A et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837

    Article  CAS  Google Scholar 

  4. Chovanec P et al (2019) Network analysis of promoter interactions reveals the hierarchical differences in genome organisation between human pluripotent states bioRxiv 2019.12.13.875286

    Google Scholar 

  5. Ji X et al (2016) 3D chromosome regulatory landscape of human pluripotent cells. Cell Stem Cell 18:262–275

    Article  CAS  Google Scholar 

  6. Pontis J et al (2019) Hominoid-specific transposable elements and KZFPs facilitate human embryonic genome activation and control transcription in naive human ESCs. Cell Stem Cell 24:724–735

    Article  CAS  Google Scholar 

  7. Theunissen TW et al (2016) Molecular criteria for defining the naive human pluripotent state. Cell Stem Cell 19:502–515

    Article  CAS  Google Scholar 

  8. Pastor WA et al (2018) TFAP2C regulates transcription in human naive pluripotency by opening enhancers. Nat Cell Biol 20:553–564

    Article  CAS  Google Scholar 

  9. Mikkelsen TS et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560

    Article  CAS  Google Scholar 

  10. Battle SL et al (2019) Enhancer chromatin and 3D genome architecture changes from naive to primed human embryonic stem cell states. Stem Cell Rep 12:1129–1144

    Article  CAS  Google Scholar 

  11. Meers MP et al (2019) Improved CUT&RUN chromatin profiling tools. Elife 8:e46314

    Article  Google Scholar 

  12. Skene PJ, Henikoff S (2017) An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6:e21856

    Article  Google Scholar 

  13. Kaya-Okur HS et al (2019) CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 10:1930

    Article  Google Scholar 

  14. Tian B, Yang J, Brasier AR (2012) Two-step cross-linking for analysis of protein-chromatin interactions. Methods Mol Biol 809:105–120

    Article  CAS  Google Scholar 

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Correspondence to Claudia I. Semprich .

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Bendall, A., Semprich, C.I. (2022). Chromatin Profiling of Human Naïve Pluripotent Stem Cells. In: Rugg-Gunn, P. (eds) Human Naïve Pluripotent Stem Cells. Methods in Molecular Biology, vol 2416. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1907-0

  • Online ISBN: 978-1-0716-1908-7

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