The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Evolutionarily Conserved Principles Predict 3D Chromatin Organization
Open accessAbstract
SUMMARY TADs, CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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Model-based Analysis of ChIP-Seq (MACS)
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
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“Recently published studies have examined the role of CTCF in the formation of loops and TADs using an auxin-mediated degradation system in mammals (Kubo et al., 2017; Nora et al., 2017).”
Cited by
Organizational principles of 3D genome architecture
Rowley, M. J., & Corces, V. G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0060-8 · Cited by 1,171
Self-citationResolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Rando, O. J., Tjian, R., & Darzacq, X. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.002 · Cited by 661
Ultrastructural Details of Mammalian Chromosome Architecture
Krietenstein, N., Abraham, S., Venev, S. V., Abdennur, N., Gibcus, J., Hsieh, T.-H. S., Parsi, K. M., Yang, L., Maehr, R., Mirny, L. A., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.003 · Cited by 622
Transcription Elongation Can Affect Genome 3D Structure
Heinz, S., Texari, L., Hayes, M. G. B., Urbanowski, M., Chang, M. W., Givarkes, N., Rialdi, A., White, K. M., Albrecht, R. A., Pache, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.047 · Cited by 453
Visualizing DNA folding and RNA in embryos at single-cell resolution
Mateo, L. J., Murphy, S. E., Hafner, A., Cinquini, I. S., Walker, C. A., & Boettiger, A. N. (2019) · Nature · doi:10.1038/s41586-019-1035-4 · Cited by 446
Metadata
- Authors
- Rowley, M. J., Nichols, M. H., Lyu, X., Ando-Kuri, M., Rivera, I. S. M., Hermetz, K., Wang, P., Ruan, Y., & Corces, V. G.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2017-09
- Volume
- 67
- Issue
- 5
- Pages
- 837-852.e7
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2745967441
- Cited by
- 555
- References
- 48
- FWCI
- 20.58
- Type
- journal article
- Language
- en
- Open access
- bronze
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