The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
CTCF-mediated functional chromatin interactome in pluripotent cells
Open accessAbstract
Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis- and 336 trans-interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.
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Cited by
Topological domains in mammalian genomes identified by analysis of chromatin interactions
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Self-citationArchitectural protein subclasses shape 3D organization of genomes during lineage commitment
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Metadata
- Authors
- Handoko, L., Xu, H., Li, G., Ngan, C. Y., Chew, E., Schnapp, M., Lee, C. W. H., Ye, C., Ping, J. L. H., Mulawadi, F., Wong, E., Sheng, J., Zhang, Y., Poh, T., Chan, C. S., Kunarso, G., Shahab, A., Bourque, G., Cacheux-Rataboul, V., Sung, W.-K., Ruan, Y., & Wei, C.-L.
- Venue
- Nature Genetics
- Published
- 2011-06-19
- Volume
- 43
- Issue
- 7
- Pages
- 630-638
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2125397535
- Cited by
- 622
- References
- 15
- FWCI
- 31.39
- Type
- journal article
- Language
- en
- Open access
- green
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- Handoko, L., Xu, H., Li, G., Ngan, C. Y., Chew, E., Schnapp, M., Lee, C. W. H., Ye, C., Ping, J. L. H., Mulawadi, F., Wong, E., Sheng, J., Zhang, Y., Poh, T., Chan, C. S., Kunarso, G., Shahab, A., Bourque, G., Cacheux-Rataboul, V., . . . Wei, C.-L. (2011). CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genetics. https://doi.org/10.1038/ng.857
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