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Schöpflin, Robert; Melo, Uirá Souto; Moeinzadeh, Hossein; Heller, David; Laupert, Verena; Hertzberg, Jakob; Holtgrewe, Manuel; Alavi, Nico; Klever, Marius-Konstantin; Jungnitsch, Julius; Comak, Emel; Türkmen, Seval; Horn, Denise; Duffourd, Yannis; Faivre, Laurence; Callier, Patrick; Sanlaville, Damien; Zuffardi, Orsetta; Tenconi, Romano; Kurtas, Nehir Edibe; Giglio, Sabrina; Prager, Bettina; Latos-Bielenska, Anna; Vogel, Ida; Bugge, Merete; Tommerup, Niels; Spielmann, Malte; Vitobello, Antonio; Kalscheuer, Vera M; Vingron, Martin; Mundlos, Stefan
Nature communications, 10/2022, Letnik: 13, Številka: 1Journal Article
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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