ABSTRACT 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

hundreds of different restriction enzyme fragment viewpoints within the same initial small input sample to uncover complex, genome-wide networks. Following optimization of the different

steps, the entire protocol can be completed within 2 weeks. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS

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FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS CAPTURE-C: A MODULAR AND FLEXIBLE APPROACH FOR HIGH-RESOLUTION CHROMOSOME CONFORMATION CAPTURE Article 04 February 2022

SYSTEMATIC EVALUATION OF CHROMOSOME CONFORMATION CAPTURE ASSAYS Article Open access 03 September 2021 ORCHESTRATING CHROMOSOME CONFORMATION CAPTURE ANALYSIS WITH BIOCONDUCTOR Article Open

access 05 February 2024 DATA AVAILABILITY All processed Nodewalk data have been deposited in the Gene Expression Omnibus (GSE76049). The ChIP and DamId-seq data were retrieved from the Gene

Expression Omnibus as follows: cLADs (GSE22428), H3K9me2 (GSE58534) and H3K4me1 (GSM1240111). Source data for Figs. 6, 7, 8 and 3, 4 are available online in refs. 24,25, respectively. The

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  Google Scholar  Download references ACKNOWLEDGEMENTS This work was supported by the Swedish Research Council (VR 03108), the Swedish Childhood Cancer Fund (PR2017-0132), the Swedish Cancer

Society (CAN 708), the Lundberg Foundation (2018-0138), Karolinska Institutet, the Novo Nordisk Foundation (NNF16OC0021512), the Cancer Society in Stockholm (2018–2021) and the KA

Wallenberg Foundation (KAW 2017.0077). We thank A. F. Woodbridge for his efforts in the initial development of the Nodewalk pipeline and R. Ohlsson for valuable discussions. AUTHOR

INFORMATION Author notes * Noriyuki Sumida Present address: Bio Systems Design Department, Bio Analytical Systems Product Division, Analytical & Medical Solution Business Group, Hitachi

High Technologies, Hitachinaka, Ibaraki, Japan * These authors contributed equally: Johanna Vestlund, Noriyuki Sumida, Rashid Mehmood. AUTHORS AND AFFILIATIONS * Department of Oncology and

Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden Johanna Vestlund, Noriyuki Sumida, Rashid Mehmood, Deeksha

Bhartiya, Shuangyang Wu & Anita Göndör Authors * Johanna Vestlund View author publications You can also search for this author inPubMed Google Scholar * Noriyuki Sumida View author

publications You can also search for this author inPubMed Google Scholar * Rashid Mehmood View author publications You can also search for this author inPubMed Google Scholar * Deeksha

Bhartiya View author publications You can also search for this author inPubMed Google Scholar * Shuangyang Wu View author publications You can also search for this author inPubMed Google

Scholar * Anita Göndör View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS J.V. updated the Nodewalk protocol and contributed to manuscript

writing; N.S. contributed to the invention of the Nodewalk assay, developed the entire protocol and contributed to the development of the analysis pipeline and manuscript writing; R.M. and

D.B. designed the submitted state of pipeline and implemented the Python code; D.B. designed the manual and tested the code; S.W. contributed to the pipeline code integration and A.G.

contributed to the invention of the Nodewalk assay and wrote the manuscript. CORRESPONDING AUTHOR Correspondence to Anita Göndör. ETHICS DECLARATIONS COMPETING INTERESTS D.B. has formed a

bioinformatics company, Genomiki Solution Ltd., that analyses high throughput data, including chromatin fibre interaction maps. PEER REVIEW PEER REVIEW INFORMATION _Nature Protocols_ thanks

Argyris Papantonis and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with

regard to jurisdictional claims in published maps and institutional affiliations. RELATED LINKS KEY REFERENCES USING THIS PROTOCOL Sumida, N. et al_. Nucleic Acids Res_. 48, 10867–10876

(2020): https://doi.org/10.1093/nar/gkaa817 Scholz, B. A. et al. _Nat. Genet_. 51, 1723–1731 (2019): https://doi.org/10.1038/s41588-019-0535-3 SUPPLEMENTARY INFORMATION SUPPLEMENTARY

INFORMATION Supplementary Note. REPORTING SUMMARY RIGHTS AND PERMISSIONS Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a

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agreement and applicable law. Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Vestlund, J., Sumida, N., Mehmood, R. _et al._ The Nodewalk assay to quantitate chromatin fiber

interactomes in very small cell populations. _Nat Protoc_ 18, 755–782 (2023). https://doi.org/10.1038/s41596-022-00774-8 Download citation * Received: 06 December 2019 * Accepted: 18 August

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