Chromatin interaction networks and higher order architectures of eukaryotic genomes

Abstract
Eukaryotic genome is, not only linearly but also spatially, organized into non‐random architecture. Though the linear organization of genes and their epigenetic descriptors are well characterized, the relevance of their spatial organization is beginning to unfold only recently. It is increasingly being recognized that physical interactions among distant genomic elements could serve as an important mean to eukaryotic genome regulation. With the advent of proximity ligation based techniques coupled with next generation sequencing, it is now possible to explore whole genome chromatin interactions at high resolution. Emerging data on genome‐wide chromatin interactions suggest that distantly located genes are not independent entities and instead cross‐talk with each other in an extensive manner, supporting the notion of “chromatin interaction networks”. Moreover, the data also advance the field to “3‐dimensional (3D) chromatin structure and dynamics”, which would enable molecular biologists to explore the spatiotemporal regulation of genome. In this article, we introduce a stepwise topological transformation of genome from 1‐dimension (1D, linear) to 2‐dimension (2D, networks) to 3‐dimension (3D, architecture) and discuss how such transformations could advance our understanding of genome biology. J. Cell. Biochem. 112: 2218–2221, 2011. © 2011 Wiley‐Liss, Inc.