Abstract
During interphase, chromosomes are relatively de-condensed in the nuclear space. Interphase chromosomes are known to occupy nuclear space in a non-random manner (chromosome territory); however, their internal structures are poorly defined. In particular, little is understood about the molecular mechanisms that govern the internal organization of interphase chromosomes. The author recently proposed that pairing (or interaction) of repetitive DNA-containing chromatin regions is a critical driving force that specifies the higher-order organization of eukaryotic chromosomes. Guided by this theoretical framework and published experimental data on the structure of interphase chromosomes and the spatial distribution of repetitive DNA in interphase nuclei, I postulate here a molecular structure of chromatin organization in interphase chromosomes. According to this model, an interphase chromosome is a chromatin mesh (or lattice) that is formed by repeat pairing (RP). The mesh consists of two types of structural components: chromosome nodes and loose chromatin fibers. Chromosome nodes are DNA repeat assemblies (RAs) that are formed via RP, while loose fibers include chromatin loops that radiate from the nodes. Different loops crosslink by RPs and form a large integrated chromatin network. I suggest that the organization of the chromatin network of a given interphase chromosome is intrinsically specified by the distribution of repetitive DNA elements on the linear chromatin. The stability of the organization is governed by the collection of RA-formed nodes, and the dynamics of the organization is driven by the assembling and disassembling of the nodes.
Highlights
The importance of chromatin organization in controlling genome activity is undisputed [1]
Based on the idea of repeat pairing (RP) and the supporting experimental evidence, I will discuss here some of the conclusions that can be made about the internal structure of chromatin organization in interphase chromosomes
The repetitive DNA-mediated chromatin mesh proposed here emphasizes the role of repetitive DNA as a structural code for the interphase chromosome organization
Summary
The importance of chromatin organization in controlling genome activity is undisputed [1]. I have recently proposed a DNA-repeat-based principle for chromatin organization, and named it CORE (chromatin organization by repetitive elements) [9] According to this hypothesis, chromatin regions with repetitive DNA in the same family tend to associate with one another and form repeat assemblies (RAs). The formation of RAs generates a molecular driving force to fold and organize chromatins within chromosomes In this way, repeats function as chromatin organizer modules. Based on the idea of RP and the supporting experimental evidence, I will discuss here some of the conclusions that can be made about the internal structure of chromatin organization in interphase chromosomes This structure, if correct, reveals a molecular organization of the chromatin in the seemingly amorphous interphase chromosomes. This chromatin organization may contain considerable information about the functional regulation of interphase chromosomes
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