Genome-wide mapping and analysis of chromosome architecture
Open accessAbstract
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects DNA replication, transcription and the repair of DNA damage. Thus, a thorough understanding of nuclear architecture is fundamental to the study of nuclear processes in eukaryotic cells. Recent years have seen rapid proliferation of technologies to investigate genome organization and function. Here, we review experimental and computational methodologies for 3D genome analysis, with special focus on recent advances in high-throughput chromatin conformation capture (3C) techniques and data analysis.
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Many TADs are composed of smaller TAD-like domains at higher resolution.
“TADs were originally discovered using Hi-C data that had ~40kb resolution, and improvements of the experimental and analytical aspects of Hi-C methods revealed that many TADs are composed of smaller TAD-like domains at higher resolution (Schmitt et al., 2016).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Schmitt et al., 2016
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High-quality genome (re)assembly using chromosomal contact data
Marie-Nelly, H., Marbouty, M., Cournac, A., Flot, J., Liti, G., Poggi-Parodi, D., Syan, S., Guillén, N., Margeot, A., Zimmer, C., et al. (2014) · Nature Communications · doi:10.1038/ncomms6695 · Cited by 165 · see citing works
Sequencing small genomic targets with high efficiency and extreme accuracy
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Two-dimensional segmentation for analyzing Hi-C data
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Global identification of yeast chromosome interactions using Genome conformation capture
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Chromatin Loop Formation in the β-Globin Locus and Its Role in Globin Gene Transcription
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“…of proximity-ligation products has been used to infer the 3D distances between a pair of DNA sequences, procedures including crosslinking, chromatin fragmentation, biotin-labelling and re-ligation can all introduce biases that complicate the interpretation of observed contact frequencies 74–76 .”
BackgroundFrom cells to chromatin: Capturing snapshots of genome organization with 5C technology
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Flagged first, then by citations
Cited by
Sorted by citations
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 · see citing works
Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
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Cai, Y., Zhang, Y., Loh, Y. P., Tng, J. Q., Lim, M. C., Cao, Z., Raju, A., Lieberman Aiden, E., Li, S., Manikandan, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-20940-y · Cited by 321 · see citing works
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“Advances in next-generation sequencing–based chromosome conformation capturing methods (3C/Hi-C) have revealed partitioning into several hundred kilobases to a few megabase-sized topologically associating domains (TADs) (6, 7).”
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
Freire-Pritchett, P., Schoenfelder, S., Várnai, C., Wingett, S. W., Cairns, J., Collier, A. J., García-Vílchez, R., Furlan-Magaril, M., Osborne, C. S., Fraser, P., et al. (2017) · eLife · doi:10.7554/elife.21926 · Cited by 161 · see citing works
“Over the last decade, chromosome conformation capture (3C) and derived methods have enabled the biochemical mapping of looping interactions to offer new insights into their architecture across different cell types (Dekker et al., 2013; de Laat and Duboule, 2013; Schmitt et al., 2016).”
BackgroundFISH-ing for captured contacts: towards reconciling FISH and 3C
Fudenberg, G., & Imakaev, M. (2017) · Nature Methods · doi:10.1038/nmeth.4329 · Cited by 141 · see citing works
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
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“Specifically, we define a bin pair (i, j) as an statistically significant bin pair if it satisfies the following three criteria simultaneously: (1) xij ≥ 12, (2) xij ?̃?ij ⁄ ≥ 2 and (3) qij < 0.”
BackgroundSelf-citationIntegrating the DNA damage and protein stress responses during cancer development and treatment
Gorgoulis, V. G., Pefani, D., Pateras, I. S., & Trougakos, I. P. (2018) · The Journal of Pathology · doi:10.1002/path.5097 · Cited by 108 · see citing works
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FIREcaller: Detecting frequently interacting regions from Hi-C data
Crowley, C., Yang, Y., Qiu, Y., Hu, B., Abnousi, A., Lipiński, J., Plewczyński, D., Wu, D., Won, H., Ren, B., et al. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.12.026 · Cited by 37 · see citing works
Self-citationChiou, J., Zeng, C., Cheng, Z., Han, J. Y., Schlichting, M., Huang, S., Wang, J., Sui, Y., Deogaygay, A., Okino, M.-L., et al. (2019) · doi:10.1101/693671 · Cited by 189 · see citing works
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- Authors
- Schmitt, A. D., Hu, M., & Ren, B.
- Affiliations
- University of California San Diego (US)
- Cleveland Clinic (US)
- Corresponding author
- Hu, Ming
- Ren, Bing
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2016-09-01
- Volume
- 17
- Issue
- 12
- Pages
- 743-755
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- PMC
- PMC5763923
- OpenAlex
- W2507209892
- Cited by
- 344
- References
- 120
- Citations by year
- 2026: 11 · 2025: 14 · 2024: 19 · 2023: 24 · 2022: 24 · 2021: 42 · 2020: 49 · 2019: 61 · 2018: 63 · 2017: 32 · 2016: 5
- FWCI
- 4.80
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U54HG006997)
- National Institute of General Medical Sciences (T32GM008666)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK107977)
- National Institute of Environmental Health Sciences (R01ES024984)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromosome organization, 3D genome organization, chromosome conformation capture, Hi-C, nuclear organization, DNA replication, transcription, DNA repair
- MeSH terms
- Animals, Chromatin, Chromosome Mapping, Chromosomes, Computer Simulation, Humans, Models, Molecular
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