2014
DOI: 10.1093/nar/gku698
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Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

Abstract: Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the gene… Show more

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Cited by 430 publications
(490 citation statements)
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References 55 publications
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“…Observations of living cells [15,16] and the "C-experiments" [17] confirm that euchromatin -the active DNA, is colocalized and separated from the inactive denser heterochromatin by an unknown mechanism. The chemical difference of the hetero-and euchromatin [16] could play a role in the chromatin separation [18], and, as first shown by Ganai et al [11], the active process that we are focusing on here too, could bring an additional contribution to the separation.Recently, two works [6, 10] modelled active colloidal particles as having higher diffusivity as their passive counterparts, by simply connecting them to a higher temperature thermostat. Both, simulations and analytical theory predict phase separation at a temperature ratio of about 30.…”
supporting
confidence: 54%
“…Observations of living cells [15,16] and the "C-experiments" [17] confirm that euchromatin -the active DNA, is colocalized and separated from the inactive denser heterochromatin by an unknown mechanism. The chemical difference of the hetero-and euchromatin [16] could play a role in the chromatin separation [18], and, as first shown by Ganai et al [11], the active process that we are focusing on here too, could bring an additional contribution to the separation.Recently, two works [6, 10] modelled active colloidal particles as having higher diffusivity as their passive counterparts, by simply connecting them to a higher temperature thermostat. Both, simulations and analytical theory predict phase separation at a temperature ratio of about 30.…”
supporting
confidence: 54%
“…It should be mentioned that a significant difference between our polymer simulations and models previously suggested by the Cavalli and Vaillant groups (Jost et al 2014) is the use of saturating interactions between inactive nucleosomes. In the case of volume interactions, all nucleosomes of the same type adjacent in 3D space will attract each other; in the case of saturating interactions, each nucleosome may attract only one neighbor.…”
Section: Discussionmentioning
confidence: 90%
“…As a result, when two segments of chromatin come into contact, the effective free energy change due to this contact depends, to first order, on the chromatin type of each segment [also Jost et al (16)]. …”
mentioning
confidence: 99%