Three-dimensional genome architecture: players and mechanisms - PubMed (original) (raw)
Review
doi: 10.1038/nrm3965. Epub 2015 Mar 11.
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- PMID: 25757416
- DOI: 10.1038/nrm3965
Review
Three-dimensional genome architecture: players and mechanisms
Ana Pombo et al. Nat Rev Mol Cell Biol. 2015 Apr.
Erratum in
- Nat Rev Mol Cell Biol. 2015 Sep;16(9):576
Abstract
The different cell types of an organism share the same DNA, but during cell differentiation their genomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. These can range from large-scale folding of whole chromosomes or of smaller genomic regions, to the re-organization of local interactions between enhancers and promoters, mediated by the binding of transcription factors and chromatin looping. The higher-order organization of chromatin is also influenced by the specificity of the contacts that it makes with nuclear structures such as the lamina. Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus.
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References
- Nature. 2011 Aug 10;476(7361):467-71 - PubMed
- Trends Genet. 2014 Jan;30(1):1-9 - PubMed
- Biochim Biophys Acta. 2009 Feb;1793(2):312-24 - PubMed
- Science. 2013 Aug 9;341(6146):660-4 - PubMed
- Biochim Biophys Acta. 2012 May;1819(5):401-10 - PubMed
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