Highly structured homolog pairing reflects functional organization of the Drosophila genome

Trans-homolog interactions encompass potent regulatory functions, which have been studied extensively in Drosophila, where homologs are paired in somatic cells and pairing-dependent gene regulation, or transvection, is well-documented. Nevertheless, the structure of pairing and whether its functional impact is genome-wide have eluded analysis. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, discovering that homologs pair relatively precisely genome-wide in addition to establishing trans-homolog domains and compartments. We also elucidated the structure of pairing with unprecedented detail, documenting significant variation across the genome. In particular, we characterized two forms: tight pairing, consisting of contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional role genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing. Overall design: This submission contains four Hi-C experiments on a Drosophila cell line: 2 biological replicates of Hi-C on a wild type sample, 2 biological replicates of Hi-C on a mock RNAi sample, 2 biological replicates of Hi-C on a Slmb RNAi sample, 2 biological replicates of Hi-C on a Top2 RNAi sample. The submission also contain 4 biological replica of a RNA-Seq experiment on a Wild Type sample.