Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes.

IF 5.3 2区 生物学 Q2 CELL BIOLOGY Journal of Molecular Cell Biology Pub Date : 2023-11-27 DOI:10.1093/jmcb/mjad042
Cibo Feng, Jin Wang, Xiakun Chu
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Abstract

The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene expression. When the cell changes its identity in the cell-fate decision-making process, extensive rearrangements of chromosome structures occur accompanied by large-scale adaptations of gene expression, underscoring the importance of chromosome dynamics in shaping genome function. Over the last two decades, rapid development of experimental methods has provided unprecedented data to characterize the hierarchical structures and dynamic properties of chromosomes. In parallel, these enormous data offer valuable opportunities for developing quantitative computational models. Here, we review a variety of large-scale polymer models developed to investigate the structures and dynamics of chromosomes. Different from the underlying modeling strategies, these approaches can be classified into data-driven ('top-down') and physics-based ('bottom-up') categories. We discuss their contributions to offering valuable insights into the relationships among the structures, dynamics, and functions of chromosomes and propose the perspective of developing data integration approaches from different experimental technologies and multidisciplinary theoretical/simulation methods combined with different modeling strategies.

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大规模的数据驱动模型和基于物理学的模型为染色体的结构、动力学和功能之间的关系提供了洞察力。
细胞核中有组织的三维染色体结构为基因表达的精确调控提供了支架。当细胞在细胞命运决策过程中改变其身份时,染色体结构会发生大范围的重新排列,同时基因表达也会发生大规模的调整,这凸显了染色体动力学在塑造基因组功能方面的重要性。过去二十年来,实验方法的快速发展为描述染色体的层次结构和动态特性提供了前所未有的数据。与此同时,这些庞大的数据也为开发定量计算模型提供了宝贵的机会。在此,我们回顾了为研究染色体结构和动力学而开发的各种大规模聚合物模型。与基本建模策略不同,这些方法可分为数据驱动型("自上而下")和物理型("自下而上")两类。我们讨论了这些方法对深入了解染色体的结构、动力学和功能之间的关系所做出的贡献,并提出了从不同的实验技术和多学科理论/模拟方法出发,结合不同的建模策略,发展数据整合方法的观点。
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来源期刊
CiteScore
9.60
自引率
1.80%
发文量
1383
期刊介绍: The Journal of Molecular Cell Biology ( JMCB ) is a full open access, peer-reviewed online journal interested in inter-disciplinary studies at the cross-sections between molecular and cell biology as well as other disciplines of life sciences. The broad scope of JMCB reflects the merging of these life science disciplines such as stem cell research, signaling, genetics, epigenetics, genomics, development, immunology, cancer biology, molecular pathogenesis, neuroscience, and systems biology. The journal will publish primary research papers with findings of unusual significance and broad scientific interest. Review articles, letters and commentary on timely issues are also welcome. JMCB features an outstanding Editorial Board, which will serve as scientific advisors to the journal and provide strategic guidance for the development of the journal. By selecting only the best papers for publication, JMCB will provide a first rate publishing forum for scientists all over the world.
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