The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Identification of alternative topological domains in chromatin
Open accessAbstract
Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries.
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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
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
Nagano, T., Lubling, Y., Stevens, T. J., Schoenfelder, S., Yaffe, E., Dean, W., Laue, E. D., Tanay, A., & Fraser, P. (2013) · Nature · doi:10.1038/nature12593 · Cited by 1,589
A map of the cis-regulatory sequences in the mouse genome
Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361 · cited 1×
“For mouse embryonic cell CTCF binding sites and chromatin modification marks, we used data by Shen et al. [19].”
MethodGenome Architecture: Domain Organization of Interphase Chromosomes
Bickmore, W. A., & van Steensel, B. (2013) · Cell · doi:10.1016/j.cell.2013.02.001 · Cited by 725
Functional implications of genome topology
Cavalli, G., & Misteli, T. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2474 · Cited by 415
Lin, Y. C., Benner, C., Mansson, R., Heinz, S., Miyazaki, K., Miyazaki, M., Chandra, V., Bossen, C., Glass, C. K., & Murre, C. (2012) · Nature Immunology · doi:10.1038/ni.2432 · Cited by 281
Cited by
Two independent modes of chromatin organization revealed by cohesin removal
Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
Dowen, J. M., Fan, Z. P., Hnisz, D., Ren, G., Abraham, B. J., Zhang, L. N., Weintraub, A. S., Schuijers, J., Lee, T. I., Zhao, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.030 · Cited by 884
Chromatin Domains: The Unit of Chromosome Organization
Dixon, J. R., Gorkin, D. U., & Ren, B. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.018 · Cited by 811
Ulianov, S. V., Khrameeva, E. E., Gavrilov, A. A., Flyamer, I. M., Kos, P., Mikhaleva, E. A., Penin, A. A., Logacheva, M. D., Imakaev, M. V., Chertovich, A., et al. (2016) · Genome Research · doi:10.1101/gr.196006.115 · Cited by 388
The Hitchhiker’s guide to Hi-C analysis: Practical guidelines
Lajoie, B. R., Dekker, J., & Kaplan, N. (2015) · Methods · doi:10.1016/j.ymeth.2014.10.031 · Cited by 385
Metadata
- Authors
- Filippova, D., Patro, R., Duggal, G., & Kingsford, C.
- Venue
- Algorithms for Molecular Biology
- Published
- 2014-01
- Volume
- 9
- Issue
- 1
- Pages
- 14-14
- ISSN
- 1748-7188 (ISSN-L)
- OpenAlex
- W2109949710
- Cited by
- 226
- References
- 6
- FWCI
- 7.18
- Type
- journal article
- Language
- en
- Open access
- gold
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- Filippova, D., Patro, R., Duggal, G., & Kingsford, C. (2014). Identification of alternative topological domains in chromatin. Algorithms for Molecular Biology. https://doi.org/10.1186/1748-7188-9-14
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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