Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity

Abstract

The eukaryotic genome is partitioned into topologically associated domains (TADs) that assemble into compartments of shared chromatin valance. This architecture is influenced by the physical constraints imposed by the DNA polymer, which restricts DNA interactions predominantly to genomic segments from the same chromosome. Here, we report a dramatic divergence from this pattern of nuclear organization that occurs during the differentiation and specification of mouse olfactory sensory neurons (OSNs). In situ HiC on FAC-sorted OSNs shows that olfactory receptor (OR) genes from numerous chromosomes make frequent, extensive, and highly specific interchromosomal contacts that strengthen with differentiation. Moreover, in terminally differentiated OSNs, >30 intergenic enhancers generate a multi-chromosomal hub that associates only with the single active OR from a pool of ~1400 genes. Our data reveal that interchromosomal interactions can form with remarkable stereotypy between like neurons, generating a regulatory landscape for stochastic, monogenic, and monoallelic gene expression.Mouse ORs are encoded by a family of ~1400 genes that are organized in 69 heterochromatic genomic clusters distributed across most chromosomes. Every mature OSN (mOSN) expresses one OR gene from one allele in a seemingly stochastic fashion 1-3 . Previous work suggested that repressive and activating interchromosomal interactions contribute to the singular OR expression 4-6 . However, these interactions have only been analyzed with the use of biased and low-throughput approaches (3C, 4C, capture HiC, and DNA FISH), which have either limited genomic resolution or restricted genomic coverage. Thus, it remains unknown how prevalent and specific these interactions are, and how they form in relationship to OSN differentiation and OR expression. Moreover, in situ HiC 7 , which reduces the occurrence of non-specific ligation events observed in dilution HiC, revealed that interchromosomal associations between non-repetitive, genic regions are extremely infrequent 8,9 , and only emerge upon depletion of cohesin complexes 10,11 . Thus, to explore the landscape of interchromosomal interactions in a biological system that likely depends on them, and to provide a conclusive answer into whether interchromosomal contacts actually occur with biologically meaningful frequency and specificity, we performed in situ HiC in distinct cell populations of the main olfactory epithelium (MOE).

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

“…Indeed, SCR transcriptional control does demonstrate proximity dependence on some scale, as SCR ablation is not compensated for by a normal copy located on the homologous chromosome (Li et al, 2014; Zhou et al, 2014). In other contexts, such as during olfactory receptor gene choice or transvection in Drosophila , regulation can occur over very large distances in cis (~80 Mb) or in trans, and transcriptional activity may be more closely tied to pairing events that promote spatial proximity, as recently demonstrated for the latter (Horta et al, 2018; Lim et al, 2018; Markenscoff-Papadimitriou et al, 2014). Hence, genomic interactions and other features of genome topology may differ in importance depending of the spatial distances navigated by enhancer-gene pairs.…”

Methods for mapping 3D chromosome architecture

“…While the reports about such contacts are increasing, the question about the functionality and importance of long-range chromatin contacts above the TAD level is still debated. While there are some examples about the role of inter-chromosomal contacts in gene expression (Apostolou and Thanos, 2008;Horta et al, 2018;Lomvardas et al, 2006;Spilianakis et al, 2005), so far there is no causal relationship known between alterations in inter-chromosomal contacts and the misregulation of genes. Studying long-range and interchromosomal contact changes in disease is the first step towards a better understanding of these contacts.…”

Interchromosomal interactions: A genomic love story of kissing chromosomes

“…However, our understanding about the formation and the function of NHCCs is still in its infancy compared with other aspects in chromatin biology. Indeed, several studies have shown examples of NHCCs, as they are detectable in many contexts (Bolzer et al, 2005; Spilianakis et al, 2005; Branco and Pombo, 2006; Lomvardas et al, 2006; Maass et al, 2012, 2018b,c; Hacisuleyman et al, 2014; Horta et al, 2018; Quinodoz et al, 2018), yet their function remains elusive.…”

“…1, C and D; Clowney et al, 2012). Recent in situ Hi-C experiments of FACS-sorted, differentiated olfactory sensory neurons determined that, at very large scales (i.e., 500-kb resolution), NHCCs between OR genes are highly specific and frequent, and that they consist of multiple different chromosomes to regulate selectively and specifically the transcription of each individual OR gene (Horta et al, 2018).…”