Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

Abstract

Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus of each cell.There are currently two distinct views of genome organization that are derived from different technologies. The first view, derived from genome-wide proximity ligation methods (e.g. Hi-C), suggests that genome organization is largely organized around chromosomes. The second view, derived from in situ imaging, suggests a central role for nuclear bodies. Yet, because microscopy and proximity-ligation methods measure different aspects of genome organization, these two views remain poorly reconciled and our overall understanding of how genomic DNA is organized within the nucleus remains incomplete. Here, we develop Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which moves away from proximity-ligation and enables genome-wide detection of higher-order DNA interactions within the nucleus. Using SPRITE, we recapitulate known genome structures identified by Hi-C and show that the contact frequencies measured by SPRITE strongly correlate with the 3-dimensional distances measured by microscopy. In addition to known structures, SPRITE identifies two major hubs of interchromosomal interactions that are spatially arranged around the nucleolus and nuclear speckles, respectively. We find that the majority of genomic regions exhibit preferential spatial association relative to one of these nuclear bodies, with regions that are highly transcribed by RNA Polymerase II organizing around nuclear speckles and transcriptionally inactive and centromereproximal regions organizing around the nucleolus. Together, our results reconcile the two distinct pictures of nuclear structure and demonstrate that nuclear bodies act as interchromosomal hubs that shape the overall 3-dimensional packaging of genomic DNA in the nucleus.

Trading Genome Vulnerability for Stable Genetic Inheritance: Active Retrotransposons Help Maintain Pericentromeric Heterochromatin Required for Faithful Cell Division

“…5A,B). This 310 suggests multiple active rRNA transcription sites are in close spatial proximity with adjacent 311 pericentromeric regions, as recently observed based on proximity ligation (Quinodoz et al 2017). 312 Importantly, we also identified CHARRs on multiple non-pericentromeric regions, suggesting 313 their potential interactions with chromatin in both cis-and trans-modes.…”

“…3A). The 256 association of rRNAs with heterochromatin agrees with a recent observation that transcriptionally 257 inert centromere-proximal regions tend to be organized around the nucleolus in 3D 258 genome (Quinodoz et al 2017). However, since rRNAs are assembled into ribosomes, rather than 259 processed into small RNAs, it is unlikely that they contribute to heterochromatin functions.…”

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, ), or the more recent GAM (Beagrie, Scialdone, Schueler, et al, ) and SPRITE (Quinodoz et al, ). 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.…”

“…Additionally, TADs appear to form higher‐order structures (meta‐TADs) (Fraser, Ferrai, Chiariello, et al, ), arranged in a hierarchy of domains‐within‐domains, extending across chromosomal scales up to comprise entire chromosomes. Chromatin also forms hubs of interchromosomal interactions as those found around the nucleolus and nuclear speckles (Quinodoz et al, , and references therein), along with hundreds of large, gene‐repressive domains associated with the nuclear lamina (LADs) that also contribute to the organization of the genome inside the nucleus (van Steensel & Belmon, ). Importantly, it has been shown that diseases, such as congenital disorders and cancer, can be linked to chromatin misfolding (Lupiáñez, Kraft, Heinrich, et al, ; Valton & Dekker, ; Weischenfeldt et al, ).…”

Pioneer Factors in Animals and Plants—Colonizing Chromatin for Gene Regulation

“…In higher eukaryotes, the genome is organized into hierarchical folding of chromosomes in highly ordered three-dimensional structures. As revealed by chromosome conformation capture (3C) assays, chromosomes are divided into territories of A (active) and B (inactive) compartments [ 82 , 83 , 84 , 85 ], which are further partitioned into topologically associating domains (TADs). Within each TAD territory, gene interactions are enriched and largely stabilized by the architectural proteins, such as CTCF [ 86 , 87 , 88 ] and cohesion [ 89 , 90 ].…”