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

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...

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Bibliographic Details
Published in:Genes & development 2019-11, Vol.33 (21-22), p.1591-1612
Main Authors: Renschler, Gina, Richard, Gautier, Valsecchi, Claudia Isabelle Keller, Toscano, Sarah, Arrigoni, Laura, Ramírez, Fidel, Akhtar, Asifa
Format: Article
Language:English
Subjects:
Algorithms
Animals
Chromosomes, Insect - genetics
Conserved Sequence
Dosage Compensation, Genetic
Drosophila - embryology
Drosophila - genetics
Embryo, Nonmammalian
Environmental Sciences
Evolution, Molecular
Gene Expression Regulation - genetics
Genome, Insect - genetics
Life Sciences
Resource Methodology
Vegetal Biology
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Summary: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 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.
ISSN:0890-9369
1549-5477
DOI:10.1101/gad.328971.119