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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

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Renschler,  Gina
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Gautier,  Richard
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Claudia,  Valsecci
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Toscano,  Sarah
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Arrigoni,  Laura
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Ramírez,  Fidel
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

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Akhtar,  Asifa
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Citation

Renschler, G., Gautier, R., Claudia, V., Toscano, S., Arrigoni, L., Ramírez, F., et al. (2019). Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling. Genes and Development, 33, 1591-1612. doi:10.1101/gad.328971.119.


Cite as: http://hdl.handle.net/21.11116/0000-0008-9374-F
Abstract
Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs), and spatial contacts between high-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservation at various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarily flexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential processes such as dosage compensation of the X chromosome.