The DOI matches its Crossref record; 47 of the 54 references it cites were found in a registry or an index.
Supercoiling in DNA and chromatin
Open accessAbstract
Supercoiling is a fundamental property of DNA and chromatin. It is modulated by polymerase and topoisomerase activities and, through regulated constraint, by DNA/chromatin binding proteins. As a non-covalent and elusive topological modification, supercoiling has proved intractable to research despite being a crucial regulator of nuclear structure and function. Recent studies have improved our understanding of the formation, regulation and organisation of supercoiling domains in vivo, and reinforce the prospect that the propagation of supercoiling can influence local and global chromatin structure. However, to further our understanding the development of new experimental tools and models are required to better dissect the mechanics of this key topological regulator.
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“However, at least as they are usually implemented, MPRAs remain limited by several factors, including the length constraints and cost of DNA synthesis or the immense complexity of shotgun libraries, the confounding effect of the reporter’s minimal promoter, and the use of episomes whose chromatin may have different properties than that of the genome189.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [189]
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Citations
Cites
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · cited 3×
“The boundaries of TADS are enriched for CTCF binding sites.”
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · cited 2×
“The boundaries of TADS are enriched for CTCF binding sites.”
Supercoiling of the DNA template during transcription.
Liu, L. F., & Wang, J. C. (1987) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.84.20.7024 · Cited by 1,877 · cited 1×
“The classic example is the ‘twin supercoiled domain’ model where elongating RNA polymerase, in unwinding the DNA, generates positive supercoiling ahead and, in rewinding the DNA, generates negative supercoiling in its wake [7,8] (Figure 1).”
Topological domain structure of the Escherichia coli chromosome.Preprint
Postow, L., Hardy, C. D., Arsuaga, J., & Cozzarelli, N. (2004) · Genes & Development · doi:10.1101/gad.1207504 · Cited by 473 · cited 1×
“The genome is also separately organised into about 500 independent 10 kb supercoiling domains with demarcating barriers stochastically distributed and dynamically maintained [19,20].”
Topoisomerases facilitate transcription of long genes linked to autism
King, I. F. G., Yandava, C., Mabb, A. M., Hsiao, J. S., Huang, H., Pearson, B. L., Calabrese, J. M., Starmer, J., Parker, J. S., Magnuson, T., et al. (2013) · Nature · doi:10.1038/nature12504 · Cited by 430 · cited 1×
“Genes that are negatively supercoiled are generally more efficiently transcribed [9,10] but topoisomerase inhibition studies [11,12 ,13,14] indicate that the accumulation of excessive positive or negative supercoiling will repress transcription.”
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures
Naughton, C., Avlonitis, N., Corless, S., Prendergast, J. G. D., Mati, I. K., Eijk, P. P., Cockroft, S. L., Bradley, M., Ylstra, B., & Gilbert, N. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2509 · Cited by 376
Self-citationHistone acetylation reduces nucleosome core particle linking number change.
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“Although in vitro studies support this concept [5] its operation in vivo is elusive [6].”
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“Condensins introduce global positive writhe into the DNA/chromatin in vitro [46] and as a result changes in supercoiling energy are thought to co-dependently drive mitotic chromosome architecture [47] and resolution in vivo.”
Transcription-dependent dynamic supercoiling is a short-range genomic force
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“To understand the nature of eukaryotic supercoiling domains, psoralen binding has been used in combination with microarrays to map the distribution of DNA supercoils across entire genomes [23] or to particular chromosomal regions [24 ,25 ].”
Ma, J., Bai, L., & Wang, M. D. (2013) · Science · doi:10.1126/science.1235441 · Cited by 324 · cited 1×
“[34 ], in a single-molecule approach, used an angular optical trap.”
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7 of the 54 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- Freeman, 1992, DNA supercoiling in chromatin structure and gene expression, Crit Rev Eukaryot Gene Expr, 2, 165
- Macvanin, 2012, Biochimica et Biophysica Acta, BBA - Gene Regul Mech, 1819, 830
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Items 101–113 of 113
Topology-dependent DNA binding
Kolbeck, P. J., Tišma, M., Analikwu, B. T., Vanderlinden, W., Dekker, C., & Lipfert, J. (2023) · bioRxiv · doi:10.1101/2023.06.30.547266 · Cited by 1
“, in the compaction and regulation of genetic information (5-9).”
BackgroundHuman centromere formation activates transcription and opens chromatin fibre structurePreprint
Naughton, C., Huidobro, C., Catacchio, C., Buckle, A., Grimes, G., Nozawa, R.-S., Purgato, S., Rocchi, M., & Gilbert, N. (2021) · bioRxiv · doi:10.1101/2021.08.01.454615 · Cited by 1
Self-citationNew Supercoiling Theory and Model of Chromosomal Structures in Eukaryotic CellsPreprint
Zhang, H., & Li, T.-H. (2018) · ChemRxiv · doi:10.26434/chemrxiv.7415207.v1 · Cited by 1
“Molecular cell 2002, 9 (6), 1183-1190.”
BackgroundInfluentialMycobacterium tuberculosis inhibitors: action and resistance
García, P. K. (2018) · FIU - Digital Commons (Florida International University) · doi:10.25148/etd.fidc007014 · Cited by 1
“(Dame, Wyman et al. 2000) 11 DNA helix in space to form higher structures, unwinding or rewinding of DNA duplexes and chromatin remodeling (Chen, Chan et al. 2013, Gilbert and Allan 2014).”
BackgroundCpG islands act as topological sinks for transcription-induced DNA supercoilingPreprint
Naughton, C., Bonato, A., Chiang, M., Corless, S., Stocks, J., Grimes, G. R., Halliday, D., Bentivoglio, A., Brackley, C., Marenduzzo, D., et al. (2026) · bioRxiv · doi:10.64898/2026.08.24.746546
“Once accessible to transcription, replication, or DNA repair machinery, the DNA duplex undergoes cycles of unwinding and rewinding, rendering it susceptible to topological stress and structural transitions collectively referred to as DNA supercoiling 1–5 .”
Self-citationZhang, M., Cañari-Chumpitaz, C., Liu, J.-F., Onoa, B., de Cleir, S., Cheng, E., Requejo, K. I., & Bustamante, C. (2026) · Molecules and Cells · doi:10.1016/j.molcel.2026.04.013
Supercoiling Enhances DNA Mobility by Reducing Threadings and Entanglements
Smrek, J., & Michieletto, D. (2020) · bioRxiv · doi:10.1101/2020.09.21.306092
Transformation of a Thermostable G-Quadruplex Structure into DNA Duplex Driven by Reverse Gyrase
Li, D.-W., Wang, Q., Liu, Y., Liu, K., Zhuge, Q., & Lv, B. (2017) · Molecules · doi:10.3390/molecules22112021
“DNA supercoiling, on the other hand, can change the structural property of double helix by unwinding or overwinding DNA double strands [29,30].”
BackgroundMultiscale analysis of poly-ADP-ribosylation dependent chromatin remodeling mechanisms at DNA breaks
Lebeaupin, T. (2017) · theses.fr (ABES) · doi:10.70675/e61e4cf3z6af7z4766z8412zde6fc6de0dbe
Duprey, A. (2016) · doi:10.70675/613a01c0z0941z407bzb188z971fd5165800
“En revanche, si l’on applique une torsion avant de le circulariser, l’ADN va devenir surenroulé positivement si la torsion est appliquée dans le même sens que l’hélice (sens droit) et négativement si elle est opposée à l’hélice (sens gauche) [37] (Figure 8 a-b).”
BackgroundStatistical mechanical model for a closed loop plectoneme with weak helix specific forces
Lee, D. J. (. (2016) · Journal of Physics: Condensed Matter · doi:10.1088/1361-648x/aa521c
Studies of Nε-Lysine Acetylation Modification on Escherichia coli Topoisomerase I
Zhou, Q. (2017) · FIU - Digital Commons (Florida International University) · doi:10.25148/etd.fidc001972
“In other word, eukaryotic DNAs are topologically equivalent to circular DNAs (Dixon et al., 2012; Gilbert and Allan, 2014; Roca, 2011a).”
Background
Metadata
- Authors
- Gilbert, N., & Allan, J.
- Affiliations
- Institute of Genetics and Cancer (GB)
- University of Edinburgh (GB)
- Corresponding author
- Gilbert, Nick
- Allan, James
- ORCID
- Gilbert, Nick
- Venue
- Current Opinion in Genetics & Development
- Publisher
- Elsevier BV
- Published
- 2014-04
- Volume
- 25
- Pages
- 15-21
- ISSN
- 0959-437X (ISSN-L)
- PMC
- PMC4042020
- OpenAlex
- W2166306420
- Cited by
- 128
- References
- 54
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 8 · 2023: 5 · 2022: 7 · 2021: 13 · 2020: 11 · 2019: 12 · 2018: 17 · 2017: 16 · 2016: 13 · 2015: 8 · 2014: 6
- FWCI
- 0.85
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Current Opinion in Genetics & Development (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- Wellcome Trust
- Medical Research Council (MR/J00913X/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- DNA supercoiling, chromatin topology, topoisomerases, DNA polymerase, DNA-binding proteins, chromatin structure, DNA topology
- MeSH terms
- Animals, Chromatin, DNA, DNA-Binding Proteins, Humans, Nucleic Acid Conformation
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