Orchestrating chromosome conformation capture analysis with Bioconductor-Reference-Cited by-同舟云学术

Orchestrating chromosome conformation capture analysis with Bioconductor

Published:2024-02-05 Issue:1 Volume:15 Page:
ISSN:2041-1723
Container-title:Nature Communications
language:en
Short-container-title:Nat Commun

Author:

Serizay Jacques^ORCID,Matthey-Doret Cyril^ORCID,Bignaud Amaury^ORCID,Baudry Lyam^ORCID,Koszul Romain^ORCID

Abstract

AbstractGenome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book (https://bioconductor.org/books/OHCA/) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.

Funder

Fondation ARC pour la Recherche sur le Cancer

Publisher

Springer Science and Business Media LLC

Link

https://www.nature.com/articles/s41467-024-44761-x.pdf

Reference69 articles.

1. Serizay, J. & Ahringer, J. Genome organization at different scales: nature, formation and function. Curr. Opin. Cell Biol. 52, 145–153 (2018).

2. Rowley, M. J. & Corces, V. G. Organizational principles of 3D genome architecture. Nat. Rev. Genet. 19, 789–800 (2018).

3. Szabo, Q., Bantignies, F. & Cavalli, G. Principles of genome folding into topologically associating domains. Sci. Adv. 5, eaaw1668 (2019).

4. Misteli, T. The self-organizing genome: principles of genome architecture and function. Cell 183, 28–45 (2020).

5. Mirny, L. & Dekker, J. Mechanisms of chromosome folding and nuclear organization: their interplay and open questions. Cold Spring Harb. Perspect. Biol. 14, a040147 (2022).

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