ArticleScientific reports2015
Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 26 citations in OpenAlex.
- Insights into the cell fate decision-making processes from chromosome structural reorganizations.Biophysics reviews · 2022Article
- Epigenetic cell memory: The gene's inner chromatin modification circuit.PLoS computational biology · 2022Article
- Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics.PLoS computational biology · 2021Article
- Quantifying epigenetic stability with minimum action paths.Physical review. E · 2020Article
- Quantifying the Stability of Coupled Genetic and Epigenetic Switches With Variational Methods.Frontiers in genetics · 2020Article
- Genomic Energy Landscapes.Biophysical journal · 2017Review
- A physical mechanism of cancer heterogeneity.Scientific reports · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell reprogramming is a process of transitions from differentiated to pluripotent cell states via transient intermediate states. Within the epigenetic landscape framework, such a process is regarded as a sequence of transitions among basins on the landscape; therefore, theoretical construction of a model landscape which exhibits experimentally consistent dynamics can provide clues to understanding epigenetic mechanism of reprogramming. We propose a minimal gene-network model of the landscape, in which each gene is regulated by an integrated mechanism of transcription-factor binding/unbinding and the collective chemical modification of histones. We show that the slow collective variation of many histones around each gene locus alters topology of the landscape and significantly affects transition dynamics between basins. Differentiation and reprogramming follow different transition pathways on the calculated landscape, which should be verified experimentally via single-cell pursuit of the reprogramming process. Effects of modulation in collective histone state kinetics on transition dynamics and pathway are examined in search for an efficient protocol of reprogramming.
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