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  Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes

Schöpflin, R., Melo, U. S., Moeinzadeh, M. H., Heller, D., Laupert, V., Hertzberg, J., et al. (2022). Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes. Nature Communications, 13: 6470. doi:10.1038/s41467-022-34053-7.

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NatureComm_Schöpflin et al_2022.pdf (Verlagsversion), 6MB
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© 2022, The Author(s)

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Schöpflin, Robert1, Autor           
Melo, Uirá Souto1, Autor           
Moeinzadeh, Mohammad Hossein2, Autor           
Heller, David3, Autor           
Laupert, Verena3, Autor           
Hertzberg, Jakob2, Autor           
Holtgrewe, Manuel, Autor
Alavi, Nico2, Autor           
Klever, Marius-Konstantin1, Autor           
Jungnitsch, Julius4, Autor           
Comak, Emel3, Autor           
Türkmen, Seval , Autor
Horn, Denise, Autor
Duffourd, Yannis , Autor
Faivre, Laurence , Autor
Callier, Patrick , Autor
Sanlaville, Damien , Autor
Zuffardi, Orsetta , Autor
Tenconi, Romano , Autor
Kurtas, Nehir Edibe , Autor
Giglio, Sabrina , AutorPrager, Bettina , AutorLatos-Bielenska, Anna , AutorVogel, Ida, AutorBugge, Merete, AutorTommerup, Niels , AutorSpielmann, Malte4, Autor           Vitobello, Antonio, AutorKalscheuer, Vera M.5, Autor           Vingron, Martin3, Autor           Mundlos, Stefan1, Autor            mehr..
Affiliations:
1Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433557              
2Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
3Transcriptional Regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
4Human Molecular Genomics (Malte Spielmann), Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_3014183              
5Chromosome Rearrangements and Disease (Vera Kalscheuer), Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385702              

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 Zusammenfassung: Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in >300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100 kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200 kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.

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Sprache(n): eng - English
 Datum: 2022-10-072022-10-29
 Publikationsstatus: Online veröffentlicht
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: DOI: 10.1038/s41467-022-34053-7
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Titel: Nature Communications
  Kurztitel : Nat. Commun.
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: London : Nature Publishing Group
Seiten: - Band / Heft: 13 Artikelnummer: 6470 Start- / Endseite: - Identifikator: ISSN: 2041-1723
CoNE: https://pure.mpg.de/cone/journals/resource/2041-1723