Dissecting Mechanisms of Epigenetic Memory Through Computational Modeling.

IF 21.3 1区 生物学 Q1 PLANT SCIENCES Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI:10.1146/annurev-arplant-070523-041445
Amy Briffa, Govind Menon, Ander Movilla Miangolarra, Martin Howard
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Abstract

Understanding the mechanistic basis of epigenetic memory has proven to be a difficult task due to the underlying complexity of the systems involved in its establishment and maintenance. Here, we review the role of computational modeling in helping to unlock this complexity, allowing the dissection of intricate feedback dynamics. We focus on three forms of epigenetic memory encoded in gene regulatory networks, DNA methylation, and histone modifications and discuss the important advantages offered by plant systems in their dissection. We summarize the main modeling approaches involved and highlight the principal conceptual advances that the modeling has enabled through iterative cycles of predictive modeling and experiments. Lastly, we discuss remaining gaps in our understanding and how intertwined theory and experimental approaches might help in their resolution.

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通过计算建模剖析表观遗传记忆机制
由于表观遗传记忆的建立和维持所涉及的系统非常复杂,因此理解表观遗传记忆的机理基础已被证明是一项艰巨的任务。在这里,我们回顾了计算建模在帮助揭示这种复杂性方面所起的作用,它允许对错综复杂的反馈动态进行剖析。我们将重点放在基因调控网络、DNA 甲基化和组蛋白修饰中编码的三种表观遗传记忆形式上,并讨论植物系统在剖析这些记忆方面的重要优势。我们总结了所涉及的主要建模方法,并强调了通过预测建模和实验的迭代循环,建模在概念上取得的主要进展。最后,我们讨论了在我们的理解中仍然存在的差距,以及理论和实验方法的相互结合如何有助于解决这些问题。植物生物学年刊》第 75 卷的最终在线出版日期预计为 2024 年 5 月。修订后的预计日期请参见 http://www.annualreviews.org/page/journal/pubdates。
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来源期刊
Annual review of plant biology
Annual review of plant biology 生物-植物科学
CiteScore
40.40
自引率
0.40%
发文量
29
期刊介绍: The Annual Review of Plant Biology is a peer-reviewed scientific journal published by Annual Reviews. It has been in publication since 1950 and covers significant developments in the field of plant biology, including biochemistry and biosynthesis, genetics, genomics and molecular biology, cell differentiation, tissue, organ and whole plant events, acclimation and adaptation, and methods and model organisms. The current volume of this journal has been converted from gated to open access through Annual Reviews' Subscribe to Open program, with all articles published under a CC BY license.
期刊最新文献
From Starfish to Gibberellins: Biosynthesis and Regulation of Plant Hormones. Green Revolution DELLA Proteins: Functional Analysis and Regulatory Mechanisms. What Are We Learning from Plant Pangenomes? Adaptation and the Geographic Spread of Crop Species. Environmental Control of Hypocotyl Elongation.
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