Chromatin Organization by Repetitive Elements (CORE): A Genomic Principle for the Higher-Order Structure of Chromosomes

Abstract

Eukaryotic genomes contain a large amount of DNA repeats (also known as repetitive DNA, repetitive elements, and repetitive sequences). Here, I propose a role of repetitive DNA in the formation of higher-order structures of chromosomes. The central idea of this theory is that chromatin regions with repetitive sequences pair with regions harboring homologous repeats and that such somatic repeat pairing (RP) assembles repetitive DNA chromatin into compact chromosomal domains that specify chromatin folding in a site-directed manner. According to this theory, DNA repeats are not randomly distributed in the genome. Instead, they form a core framework that coordinates the architecture of chromosomes. In contrast to the viewpoint that DNA repeats are genomic ‘junk’, this theory advocates that repetitive sequences are chromatin organizer modules that determine chromatin-chromatin contact points within chromosomes. This novel concept, if correct, would suggest that DNA repeats in the linear genome encode a blueprint for higher-order chromosomal organization.

Widespread occurrence of power-law distributions in inter-repeat distances shaped by genome dynamics

“…In a recent work (Tang, 2011), it is also proposed that repeats may coordinate the higher order structure of chromatine. By this work, evidence is brought that disparate repeats of the same family often cluster in 3-D space inside nucleus, by means of "repeat pair" interactions.…”

Long-Range Order and Fractality in the Structure and Organization of Eukaryotic Genomes

“…The predicted scaling features of the fractal globule have been quantitatively verified by Hi-C and 3D-FISH (Lieberman-Aiden et al, 2009;MateosLangerak et al, 2009). Recently the 3D clustering of repeats belonging to the same family due to repeat pair interactions has led to the suggestions that such repeats coordinate the chromatin higher structure (Tang, 2011). Presumably, fractality and long-range order initially developed through neutral genome dynamics such as the ones related to repeat proliferation discussed in this chapter.…”

A Study of Fractality and Long-Range Order in the Distribution of Transposable Elements in Eukaryotic Genomes Using the Scaling Properties of Block Entropy and Box-Counting

“…The predicted scaling features of the fractal globule have been quantitatively verified by a combination of molecular biology and computational techniques [39,43]. Recently, the 3D clustering of repeats belonging to the same family due to repeat pair interactions has led to the suggestions that such repeats coordinate and maintain the chromatin higher structure [44]. Presumably, fractality and long-rangeness initially developed through neutral genome dynamics such as the ones related to repeat proliferation we discussed, and subsequently were preserved by selective forces, as this structure is intertwined with multiple genomic functions.…”