A decade of 3C technologies: insights into nuclear organization.
By E. de Wit, W. de Laat. Genes & Development, 2012
723 citations recorded by the source corpus.
Over the past 10 years, the development of chromosome conformation capture (3C) technology and the subsequent genomic variants thereof have enabled the analysis of nuclear organization at an unprecedented resolution and throughput. The technology relies on the original and, in hindsight, remarkably simple idea that digestion and religation of fixed chromatin in cells, followed by the quantification of ligation junctions, allows for the determination of DNA contact frequencies and insight into chromosome topology. Here we evaluate and compare the current 3C-based methods (including 4C [chromosome conformation capture-on-chip], 5C [chromosome conformation capture carbon copy], HiC, and ChIA-PET), summarize their contribution to our current understanding of genome structure, and discuss how shape influences genome function.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/82f78762b4eb1b98e2ef57f29ec8af371cce7dd1
How researchers see this paper
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In Molecular Biology
- Marinka Zitnik
- Jure Leskovec
- Anna Goldenberg
- Michael M. Hoffman
- Francis Nguyen
- Job Dekker
- B. Lajoie
- J. Wysocka
Citations in the corpus
- Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities (2018, background): “[76, 77] Hi-ChIP long-range interactions and associated protein Combines Hi-C and ChIP-seq.”
- HiC-Pro: an optimized and flexible pipeline for Hi-C data processing (2015, background): “The use of Hi-C has notably changed our vision of genome organization and its impact on chromatin and gene regulation [1, 2].”
- Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin (2016, methodology): “High-throughput methods for assaying chromatin interactions now exist, including paired-end tag sequencing (ChIA-PET) 28 and extensions of the chromosome conformation capture (3C) assay 29 (5C and Hi-C) 30,31 .”
- Modification of enhancer chromatin: what, how and why? (2013, background): “Among the two, the looping model has gained extensive support with the emergence of technologies such as chromosome conformation capture (3C) and its derivatives 4C and 5C (reviewed in de Wit and de Laat, 2012; Gibcus and Dekker, 2013).”