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

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.

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2019
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 Creators:
Renschler, Gina1, Author              
Gautier, Richard1, Author
Claudia, Valsecci1, Author              
Toscano, Sarah1, Author              
Arrigoni, Laura1, Author
Ramírez, Fidel1, 2, Author              
Akhtar, Asifa1, Author              
Affiliations:
1Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243640              
2Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society, ou_40046              

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Free keywords: dosage compensation, HiC, X chromosome, chromsome topology
 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.

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Language(s): eng - English
 Dates: 20192019-10-10
 Publication Status: Published online
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1101/gad.328971.119
 Degree: -

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Title: Genes and Development
Source Genre: Journal
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Publ. Info: Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 33 Sequence Number: - Start / End Page: 1591 - 1612 Identifier: ISSN: 0890-9369
CoNE: https://pure.mpg.de/cone/journals/resource/954925557453