Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

Abstract

Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.

3D Genome Structure Variation Across Cell Types Captured by Integrating Multi-omics

“…This suggests that a major mechanism controlling cell identity is sequestering different regions to the nuclear lamina. This result is in line with the recent observations from SPRITE that anchoring to nuclear bodies such as active speckles or the lamina is a major organizing factor of genome structure [28]. Here, we further extend this concept by finding that this is not only true within a single cell type, but that switches in this anchoring are the definitive difference in chromosome structure between cell types.…”

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

“…Hi‐C and other recent methods, such as genome architecture mapping (GAM), split‐pool recognition of interactions by tag extension, and the recently described method of super‐resolution chromatin tracing have allowed the 3D modeling of a hierarchy of genome structures from the level of individual genes to TADs, CTs and entire 3D genomes (Figure D‐F). Most importantly, results of 1D mapping of structurally and functionally relevant proteins distributed along the linear DNA can be immediately integrated into such 3D models.…”

“…Hi-C and other recent methods, such as genome architecture mapping (GAM), 66 split-pool recognition of interactions by tag extension 67 (2) Nucleosome-free region are formed at an enhancer and at a proximal promoter providing platforms for the recruitment of protein complexes essential for transcriptional regulation. (3/4) The enhancer recruits a pre-initiation complex (PIC) and mediator.…”

Models of polymer physics for the architecture of the cell nucleus

“…The investigation of the 3D structure of chromosomes in the nucleus of cells, and its functional implications, has been revolutionized by new technologies such as Hi-C (Lieberman-Aiden, van Berkum, Williams, et al, 2009), or the more recent GAM (Beagrie, Scialdone, Schueler, et al, 2017) and SPRITE (Quinodoz et al, 2018). Such technologies allow to measure the frequency of physical contacts between deoxyribonucleic acid (DNA) sites genome-wide, returning for instance the network of interactions formed by regulatory regions and their target genes.…”