Abstract
Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals.
Highlights
Associating domains (TADs) are fundamental elements of the eukaryotic genomic structure
Since the chromosome structure in eukaryotic cells is known to change significantly during the cell cycle[21], we sought to minimize the variability in our examination of the genomic structure of the model eukaryote, D. melanogaster, by studying cells that were arrested at the G1/S boundary
We found that BEAF-32, Chromator, and CP190 are each significantly enriched at the boundaries of the Topologically associating domains (TADs) (Supplementary Fig. 4a) while no other insulator protein exhibits such significant enrichment at these TAD borders (Supplementary Fig. 4a)
Summary
Associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. While most of the previously identified TADs, primarily enriched for inactive chromatin, are resolved as higher-order assemblages of smaller TADs, unexpectedly, the previously identified inter-TAD regions, thought to be unstructured, are composed of a string of well-defined small TADs with limited near-range inter-TAD contacts, a feature that can be identified in mammalian cells. Taken together, these results strongly suggest that several of the most basic features of the higher-order genome architecture are conserved from insects to mammals
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