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

MPG-Autoren

Renschler, Gina
Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;
External Organizations;

Richard, Gautier
Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;
External Organizations;

Keller Valsecchi, Claudia Isabelle
Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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

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

Ramírez, Fidel
Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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

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Zitation

Renschler, G., Richard, G., Keller Valsecchi, C. I., 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.

Zusammenfassung

Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensionalgenome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C datafor studying genome topology in three distantly related Drosophila species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately everysix genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs), and spatial contacts betweenhigh-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservationat various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarilyflexible, 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 essentialprocesses such as dosage compensation of the X chromosome.