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

Abstract

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.

Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3

“…However, the general applicability of this concept remains under investigation, as disruption of TADs and enhancer-promoter interactions are not always accompanied by changes in expression. Studies in Drosophila 7 and in human congenital chromothrypsis cases 8 indicate indeed a degree of robustness of the genome against such events.…”

Disruption of regulatory domains and novel transcripts as disease‐causing mechanisms

“…This study reported that while the majority of breakpoints reshuffle TADs, most genes located 200‐kb around a breakpoint do not show significant expression changes. [ 109 ] These data suggest that the enhancer adoption mechanism may be a rare cause of disease.…”

Complex structural variation is prevalent and highly pathogenic in pediatric solid tumors

“…Alternatively, the umbrella term “chromoanagenesis” can be used to encompass a spectrum of complex SVs resulting in rearranged derivative chromosomes. Long-read and Hi-C data of germline genomes also support this diversity of rearrangements and categorization into chromothripsis-like and chromoplexy-like patterns [10]. Chromothripsis is characterized by DNA shattering and haphazard repair in which genomic fragments are randomly joined, resulting in many interleaved SVs and an oscillating CN pattern with losses [11].…”

“…It can result in fusion genes such as EWSR1::FLI1 and is thought to arise when DNA damage occurs during co-localization of chromosomes in transcription hubs [1]. Both chromothripsis and chromoplexy can result in derivative chromosomes, differing mainly in the presence or absence of large copy number changes [10, 12].…”