| Full text | |
| Author(s): |
Cheng, Ryan R.
[1]
;
Contessoto, Vinicius G.
[1, 2]
;
Aiden, Erez Lieberman
[1, 3]
;
Wolynes, Peter G.
[4, 1, 5, 6]
;
Di Pierro, Michele
[1, 7]
;
Onuchic, Jose N.
[4, 1, 5, 6]
Total Authors: 6
|
| Affiliation: | [1] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 - USA
[2] Brazilian Ctr Res Energy & Mat CNPEM, Brazilian Biorenewables Natl Lab LNBR, Campinas - Brazil
[3] Baylor Coll Med, Ctr Genome Architecture, Houston, TX 77030 - USA
[4] Rice Univ, Dept Chem, Houston, TX 77005 - USA
[5] Rice Univ, Dept Biosci, Houston, TX 77005 - USA
[6] Rice Univ, Dept Phys & Astron, Houston, TX 77005 - USA
[7] Northeastern Univ, Dept Phys, Boston, MA 02115 - USA
Total Affiliations: 7
|
| Document type: | Journal article |
| Source: | eLIFE; v. 9, OCT 13 2020. |
| Web of Science Citations: | 0 |
| Abstract | |
Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscopy. We demonstrate using machine learning and polymer physics simulations that epigenetic information can be used to predict the structural ensembles of multiple human cell lines. Theory predicts that chromosome structures are fluid and can only be described by an ensemble, which is consistent with the observation that chromosomes exhibit no unique fold. Nevertheless, our analysis of both structures from simulation and microscopy reveals that short segments of chromatin make twostate transitions between closed conformations and open dumbbell conformations. Finally, we study the conformational changes associated with the switching of genomic compartments observed in human cell lines. The formation of genomic compartments resembles hydrophobic collapse in protein folding, with the aggregation of denser and predominantly inactive chromatin driving the positioning of active chromatin toward the surface of individual chromosomal territories. (AU) | |
| FAPESP's process: | 17/09662-7 - Rational Evolution by Computational Methods Applied in Enzymes Related to Bioethanol Production |
| Grantee: | Vinícius de Godoi Contessoto |
| Support Opportunities: | Scholarships abroad - Research Internship - Post-doctor |
| FAPESP's process: | 16/13998-8 - Rational evolution by computational methods applied to predict mutations in enzymes to biofuels production |
| Grantee: | Vinícius de Godoi Contessoto |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |