Chromosome territories and the global regulation of the genome

• Published in: Genes chromosomes & cancer Vol. 58; no. 7; pp. 407 - 426
• Main Authors: Fritz, Andrew J., Sehgal, Nitasha, Pliss, Artem, Xu, Jinhui, Berezney, Ronald
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01-07-2019; Wiley Subscription Services, Inc
• Subjects: Animals; Cancer; Cell cycle; Cell Nucleus - genetics; Cell Nucleus - ultrastructure; Chromatin; Chromatin - genetics; Chromatin - ultrastructure; Chromosome translocations; Chromosomes - genetics; Chromosomes - ultrastructure; Computed tomography; Disruption; Enhancers; Gene expression; Gene Expression Regulation - genetics; Gene Expression Regulation - physiology; Genes; Genome; Genomes; Humans; Nuclear transport; Nucleosomes; Structure-function relationships; Topology; Transcription activation
• ISSN: 1045-2257; 1098-2264
• DOI: 10.1002/gcc.22732

Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains (CD) or topologically associating domains (TADs) to higher level compartments culminating in chromosome territories (CT). Microscopic and sequencing techniques have substantiated chromatin organization as a critical factor regulating gene expression. For example, enhancers loop back to interact with their target genes almost exclusively within TADs, distally located coregulated genes reposition into common transcription factories upon activation, and Mbp CDs exhibit dynamic motion and configurational changes in vivo. A longstanding question in the nucleus field is whether an interactive nuclear matrix provides a direct link between structure and function. The findings of nonrandom radial positioning of CT within the nucleus suggest the possibility of preferential interaction patterns among populations of CT. Sequential labeling up to 10 CT followed by application of computer imaging and geometric graph mining algorithms revealed cell‐type specific interchromosomal networks (ICN) of CT that are altered during the cell cycle, differentiation, and cancer progression. It is proposed that the ICN correlate with the global level of genome regulation. These approaches also demonstrated that the large scale 3‐D topology of CT is specific for each CT. The cell‐type specific proximity of certain chromosomal regions in normal cells may explain the propensity of distinct translocations in cancer subtypes. Understanding how genes are dysregulated upon disruption of the normal “wiring” of the nucleus by translocations, deletions, and amplifications that are hallmarks of cancer, should enable more targeted therapeutic strategies.