The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures
Open accessAbstract
DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling, we used biotinylated trimethylpsoralen as a DNA structure probe to show that the human genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF insulator protein–binding sites. Underwound domains are transcriptionally active and enriched in topoisomerase I, 'open' chromatin fibers and DNase I sites, but they are depleted of topoisomerase II. Furthermore, DNA supercoiling affects additional levels of chromatin compaction as underwound domains are cytologically decondensed, topologically constrained and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation, providing an evolutionary purpose for clustering genes along chromosomes.
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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
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
Chromatin organization is a major influence on regional mutation rates in human cancer cells
Schuster-Böckler, B., & Lehner, B. (2012) · Nature · doi:10.1038/nature11273 · Cited by 657
Stock, J. K., Giadrossi, S., Casanova, M., Brookes, E., Vidal, M., Koseki, H., Brockdorff, N., Fisher, A. G., & Pombo, A. (2007) · Nature Cell Biology · doi:10.1038/ncb1663 · Cited by 650
Cited by
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
3D structures of individual mammalian genomes studied by single-cell Hi-C
Stevens, T. J., Lando, D., Basu, S., Atkinson, L. P., Cao, Y., Lee, S. F., Leeb, M., Wohlfahrt, K. J., Boucher, W., O’Shaughnessy-Kirwan, A., et al. (2017) · Nature · doi:10.1038/nature21429 · Cited by 832
Topoisomerases facilitate transcription of long genes linked to autism
King, I. F., Yandava, C. N., Mabb, A. M., Hsiao, J. S., Huang, H.-S., Pearson, B. L., Calabrese, J. M., Starmer, J., Parker, J. S., Magnuson, T., et al. (2013) · Nature · doi:10.1038/nature12504 · Cited by 438
Condensin-based chromosome organization from bacteria to vertebrates
Hirano, T. (2016) · Cell · doi:10.1016/j.cell.2016.01.033 · Cited by 389
Genome Organization Drives Chromosome Fragility
Canela, A., Maman, Y., Jung, S., Wong, N., Callen, E., Day, A., Kieffer-Kwon, K.-R., Pekowska, A., Zhang, H., Rao, S. S. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.034 · Cited by 383
Metadata
- Authors
- Naughton, C., Avlonitis, N., Corless, S., Prendergast, J. G., Mati, I. K., Eijk, P. P., Cockroft, S. L., Bradley, M., Ylstra, B., & Gilbert, N.
- Venue
- Nature Structural & Molecular Biology
- Published
- 2013-02-17
- Volume
- 20
- Issue
- 3
- Pages
- 387-395
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W2095955242
- Cited by
- 383
- References
- 4
- FWCI
- 13.31
- Type
- journal article
- Language
- en
- Open access
- green
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- Naughton, C., Avlonitis, N., Corless, S., Prendergast, J. G., Mati, I. K., Eijk, P. P., Cockroft, S. L., Bradley, M., Ylstra, B., & Gilbert, N. (2013). Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures. Nature Structural & Molecular Biology. https://doi.org/10.1038/nsmb.2509
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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