The Nodewalk assay to quantitate chromatin fiber interactomes in very small cell populations

The chromosome conformation capture method and its derivatives, such as circularized chromosome conformation capture, carbon copy chromosome conformation capture, high-throughput chromosome conformation capture and capture high-throughput chromosome conformation capture, have pioneered our understan...

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Veröffentlicht in:Nature protocols 2023-03, Vol.18 (3), p.755-782
Hauptverfasser: Vestlund, Johanna, Sumida, Noriyuki, Mehmood, Rashid, Bhartiya, Deeksha, Wu, Shuangyang, Göndör, Anita
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Sprache:eng
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Zusammenfassung:The chromosome conformation capture method and its derivatives, such as circularized chromosome conformation capture, carbon copy chromosome conformation capture, high-throughput chromosome conformation capture and capture high-throughput chromosome conformation capture, have pioneered our understanding of the principles of chromosome folding in the nucleus. These technical advances, however, cannot precisely quantitate interaction frequency in very small input samples. Here we describe a protocol for the Nodewalk assay, which is based on converting chromosome conformation capture DNA samples to RNA and subsequently to cDNA using strategically placed primers. This pipeline enables the quantitative analyses of chromatin fiber interactions without compromising its sensitivity down to
ISSN:1754-2189
1750-2799
1750-2799
DOI:10.1038/s41596-022-00774-8