From nucleosomes to compartments: physicochemical interactions underlying chromatin organization

From nucleosomes to compartments: physicochemical interactions underlying chromatin organization

2024 July | Shuming Liu, Advait Athreya, Zhuohan Lao, Bin Zhang
Chromatin organization is crucial for cellular function by regulating access to genetic information. Understanding chromatin folding is challenging due to its complex multiscale nature. In vitro studies have revealed the structure of nucleosomes and their interactions, while in vivo studies have characterized chromatin organization at the whole chromosome level, revealing features like chromatin loops, topologically associating domains (TADs), and nuclear compartments. However, bridging in vitro and in vivo studies remains challenging. The role of internucleosomal interactions in chromatin folding is debated, with some studies suggesting that these interactions are strong enough to influence chromatin structure in vivo. Recent advances in experimental and computational techniques have provided insights into the strength of internucleosomal interactions, showing values significantly exceeding thermal energy (k_BT). Computational modeling has also contributed to understanding chromatin structure and interactions. At larger scales, chromatin organization has been studied using techniques like Hi-C, revealing features such as chromatin loops and TADs. The complexity of chromatin folding involves multiple factors, including intrinsic interactions between nucleosomes and the influence of other proteins. The article reviews experimental and computational studies at various length scales, highlighting the significance of intrinsic interactions between nucleosomes in chromatin folding in vivo. It also discusses the role of microphase separation in chromatin organization, driven by internucleosomal interactions, and how this contributes to the formation of chromatin compartments. The study emphasizes the importance of physicochemical interactions between nucleosomes in understanding chromatin folding mechanisms.Chromatin organization is crucial for cellular function by regulating access to genetic information. Understanding chromatin folding is challenging due to its complex multiscale nature. In vitro studies have revealed the structure of nucleosomes and their interactions, while in vivo studies have characterized chromatin organization at the whole chromosome level, revealing features like chromatin loops, topologically associating domains (TADs), and nuclear compartments. However, bridging in vitro and in vivo studies remains challenging. The role of internucleosomal interactions in chromatin folding is debated, with some studies suggesting that these interactions are strong enough to influence chromatin structure in vivo. Recent advances in experimental and computational techniques have provided insights into the strength of internucleosomal interactions, showing values significantly exceeding thermal energy (k_BT). Computational modeling has also contributed to understanding chromatin structure and interactions. At larger scales, chromatin organization has been studied using techniques like Hi-C, revealing features such as chromatin loops and TADs. The complexity of chromatin folding involves multiple factors, including intrinsic interactions between nucleosomes and the influence of other proteins. The article reviews experimental and computational studies at various length scales, highlighting the significance of intrinsic interactions between nucleosomes in chromatin folding in vivo. It also discusses the role of microphase separation in chromatin organization, driven by internucleosomal interactions, and how this contributes to the formation of chromatin compartments. The study emphasizes the importance of physicochemical interactions between nucleosomes in understanding chromatin folding mechanisms.
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[slides] From Nucleosomes to Compartments%3A Physicochemical Interactions Underlying Chromatin Organization. | StudySpace