Cell-specific long-range low-frequency interactions regulate the higher-order architecture of the Drosophila genome

ANDRÉS M. CARDOZO GIZZI; DIEGO I. CATTONI, DELPHINE CHAMOUSSET; MARIYA GEORGIEVA; ALESSANDRO VALERI; DELPHINE CHAMOUSSET; GIACOMO CAVALLI; MARCELO NOLLMANN

Lucca

Congreso; Gordon Research Conference - Chromosome Dynamics; 2017

The multi-scale organization of eukaryotic genomes regulate cellular identity and tissue-specific functions (Gilbert and Fraser, 2015; de Laat and Duboule, 2013; Sexton and Cavalli, 2015). At the kilo-megabase scales, genomes are partitioned into self-interacting modules or topologically associated domains (TADs) (Dixon et al., 2012; Nora et al., 2012; Sexton et al., 2012). TADs formation seems to require specific looping interactions between TAD borders (Hug et al., 2017; Rao et al., 2015), while association of TADs can lead to the formation of active/repressed compartments (Dekker et al., 2013). These structural levels are often seen as highly stable over time, however, recent studies have reported different degrees of heterogeneity (Flyamer et al., 2017; Giorgetti et al., 2014). Access to single-cell absolute probability contact measurements and efficient detection of low-frequency, long-range interactions is essential to unveil the multiscale dynamic behaviour of chromatin. Here, we combined super-resolution microscopy with state-of-the-art DNA labeling methods to reveal the stochasticity in multiscale organization of chromosomes in different cell-types and developmental stages in Drosophila. Remarkably, we found that stochasticity is present at all levels of chromosome architecture. Contacts between consecutive TAD borders is highly infrequent, independently of TAD size, epigenetic state, or cell type. Moreover, long-range contact probabilities between non-consecutive barriers, the overall folding of chromosomes, and the clustering of epigenetic domains into active/repressed compartments displayed different degrees of stochasticity that depended on cell-type. Overall, our results show that genomes, unlike proteins, display structural variability that is differentially modulated at multiple scales, reflecting cell-type specific expression programs. We anticipate that our results and methods will be a starting point for more sophisticated studies to understand how this highly variable, multi-scale organization can ensure the maintenance of stable transcriptional programs through cell division and during development, and guide new statistical models of genome architecture.