The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
Open accessAbstract
Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods. FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde cross-linking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organization, but this has not been tested extensively. We investigated the murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental and activity states and in the presence or absence of epigenetic regulators. We identified situations in which the two data sets are concordant but found other conditions under which chromatin topographies extrapolated from 5C or FISH data are not compatible. We suggest that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart, influenced by nuclear environment and chromatin composition. We conclude that results obtained at high resolution with either 3C methods or FISH alone must be interpreted with caution and that views about genome organization should be validated by independent methods.
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Citations
Cites
Topological domains in mammalian genomes identified by analysis of chromatin interactions
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Spatial partitioning of the regulatory landscape of the X-inactivation centre
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A high-resolution map of the three-dimensional chromatin interactome in human cells
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Architectural protein subclasses shape 3D organization of genomes during lineage commitment
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Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
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A Regulatory Archipelago Controls Hox Genes Transcription in Digits
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“…and ‘‘looping’’ between long-range enhancers and their target genes (Montavon et al. 2011; Sanyal et al. 2012; Andrey et al. 2013; Berlivet et al. 2013; Hughes et al. 2014)—and between sites bound by proteins involved in chromosome architecture (Philips-Cremins et al. 2013; Seitan et al. 2013;…”
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Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003
Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174
Long-range enhancer–promoter contacts in gene expression control
Schoenfelder, S., & Fraser, P. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0128-0 · Cited by 1,102
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.024 · Cited by 892
Complex multi-enhancer contacts captured by genome architecture mapping
Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C. A., Chotalia, M., Xie, S. Q., Barbieri, M., de Santiago, I., Lavitas, L.-M., Branco, M. R., et al. (2017) · Nature · doi:10.1038/nature21411 · Cited by 715
Self-citation
Metadata
- Authors
- Williamson, I., Berlivet, S., Eskeland, R., Boyle, S., Illingworth, R. S., Paquette, D., Dostie, J., & Bickmore, W. A.
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2014-12-15
- Volume
- 28
- Issue
- 24
- Pages
- 2778-2791
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- OpenAlex
- W2101754326
- Cited by
- 234
- References
- 15
- Type
- posted content
- Language
- en
- Open access
- diamond
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- Williamson, I., Berlivet, S., Eskeland, R., Boyle, S., Illingworth, R. S., Paquette, D., Dostie, J., & Bickmore, W. A. (2014). Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes & Development. https://doi.org/10.1101/gad.251694.114
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