Literature DB >> 24580158

Bifurcation in epigenetics: implications in development, proliferation, and diseases.

Daniel Jost1.   

Abstract

Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of biochemical marks on chromatin. Here, we develop a stochastic model that describes the dynamics of epigenetic marks along a given DNA region. Through mathematical analysis, we show the emergence of bistable and persistent epigenetic states from the cooperative recruitment of modifying enzymes. We also find that the dynamical system exhibits a critical point and displays, in the presence of asymmetries in recruitment, a bifurcation diagram with hysteresis. These results have deep implications for our understanding of epigenetic regulation. In particular, our study allows one to reconcile within the same formalism the robust maintenance of epigenetic identity observed in differentiated cells, the epigenetic plasticity of pluripotent cells during differentiation, and the effects of epigenetic misregulation in diseases. Moreover, it suggests a possible mechanism for developmental transitions where the system is shifted close to the critical point to benefit from high susceptibility to developmental cues.

Mesh:

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Year:  2014        PMID: 24580158     DOI: 10.1103/PhysRevE.89.010701

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  12 in total

Review 1.  Erase and Rewind: Epigenetic Conversion of Cell Fate.

Authors:  Georgia Pennarossa; Alessandro Zenobi; Cecilia E Gandolfi; Elena F M Manzoni; Fulvio Gandolfi; Tiziana A L Brevini
Journal:  Stem Cell Rev Rep       Date:  2016-04       Impact factor: 5.739

2.  Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance.

Authors:  Daniel Jost; Cédric Vaillant
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

3.  Quantifying epigenetic stability with minimum action paths.

Authors:  Amogh Sood; Bin Zhang
Journal:  Phys Rev E       Date:  2020-06       Impact factor: 2.529

Review 4.  Mechanisms and Functions of Chromosome Compartmentalization.

Authors:  Erica M Hildebrand; Job Dekker
Journal:  Trends Biochem Sci       Date:  2020-02-18       Impact factor: 13.807

5.  Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory.

Authors:  Amith Z Abdulla; Cédric Vaillant; Daniel Jost
Journal:  Nucleic Acids Res       Date:  2022-08-26       Impact factor: 19.160

Review 6.  Reprogramming of cell fate: epigenetic memory and the erasure of memories past.

Authors:  Buhe Nashun; Peter W S Hill; Petra Hajkova
Journal:  EMBO J       Date:  2015-03-27       Impact factor: 11.598

Review 7.  Perspectives: using polymer modeling to understand the formation and function of nuclear compartments.

Authors:  N Haddad; D Jost; C Vaillant
Journal:  Chromosome Res       Date:  2017-01-14       Impact factor: 5.239

8.  Quantifying the Stability of Coupled Genetic and Epigenetic Switches With Variational Methods.

Authors:  Amogh Sood; Bin Zhang
Journal:  Front Genet       Date:  2021-01-22       Impact factor: 4.599

9.  Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains.

Authors:  Daniel Jost; Pascal Carrivain; Giacomo Cavalli; Cédric Vaillant
Journal:  Nucleic Acids Res       Date:  2014-08-04       Impact factor: 16.971

10.  Epigenetic Transitions and Knotted Solitons in Stretched Chromatin.

Authors:  D Michieletto; E Orlandini; D Marenduzzo
Journal:  Sci Rep       Date:  2017-11-07       Impact factor: 4.379

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