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Transferable model for chromosome architecture

Di Pierro, Michele ; Zhang, Bin ; Aiden, Erez Lieberman ; Wolynes, Peter G. ; Onuchic, José N.

Proceedings of the National Academy of Sciences - PNAS, 2016-10, Vol.113 (43), p.12168-12173 [Periódico revisado por pares]

United States: National Academy of Sciences

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  • Título:
    Transferable model for chromosome architecture
  • Autor: Di Pierro, Michele ; Zhang, Bin ; Aiden, Erez Lieberman ; Wolynes, Peter G. ; Onuchic, José N.
  • Assuntos: Biological Sciences ; Cells ; Chromatin ; Chromatin - genetics ; Chromatin - ultrastructure ; Chromosomes ; Chromosomes - genetics ; Chromosomes - ultrastructure ; Computer simulation ; Genome, Human ; Genomes ; Humans ; Mathematical models ; Models, Theoretical ; Molecular Conformation ; Molecular Dynamics Simulation ; Physical Sciences
  • É parte de: Proceedings of the National Academy of Sciences - PNAS, 2016-10, Vol.113 (43), p.12168-12173
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
    Author contributions: M.D.P., B.Z., E.L.A., P.G.W., and J.N.O. designed research; M.D.P. and B.Z. performed research; M.D.P. and B.Z. contributed new reagents/analytic tools; M.D.P., B.Z., E.L.A., P.G.W., and J.N.O. analyzed data; and M.D.P., B.Z., E.L.A., P.G.W., and J.N.O. wrote the paper.
    Reviewers: J.L., University of Illinois at Chicago; and T.S., New York University.
    Contributed by José N. Onuchic, August 16, 2016 (sent for review July 1, 2016; reviewed by Jie Liang and Tamar Schlick)
    1M.D.P. and B.Z. contributed equally to this work.
  • Descrição: In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. We report a theoretical model for chromatin (Minimal Chromatin Model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. First, we trained our energy function using the Hi-C contact map of chromosome 10 from human GM12878 lymphoblastoid cells. Then, we used the model to perform molecular dynamics simulations producing an ensemble of 3D structures for all GM12878 autosomes. Finally, we used these 3D structures to generate contact maps. We found that simulated contact maps closely agree with experimental results for all GM12878 autosomes. The ensemble of structures resulting from these simulations exhibited unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories.
  • Editor: United States: National Academy of Sciences
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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