Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases

Abstract

Genome-wide analysis methods, such as array comparative genomic hybridization (CGH) and whole-genome sequencing (WGS), have greatly advanced the identification of structural variants (SVs) in the human genome. However, even with standard high-throughput sequencing techniques, complex rearrangements with multiple breakpoints are often difficult to resolve, and predicting their effects on gene expression and phenotype remains a challenge. Here, we address these problems by using high-throughput chromosome conformation capture (Hi-C) generated from cultured cells of nine individuals with developmental disorders (DDs). Three individuals had previously been identified as harboring duplications at the SOX9 locus and six had been identified with translocations. Hi-C resolved the positions of the duplications and was instructive in interpreting their distinct pathogenic effects, including the formation of new topologically associating domains (neo-TADs). Hi-C was very sensitive in detecting translocations, and it revealed previously unrecognized complex rearrangements at the breakpoints. In several cases, we observed the formation of fused-TADs promoting ectopic enhancer-promoter interactions that were likely to be involved in the disease pathology. In summary, we show that Hi-C is a sensible method for the detection of complex SVs in a clinical setting. The results help interpret the possible pathogenic effects of the SVs in individuals with DDs.

A cookbook for DNase Hi-C

“…This dependence of chromatin contacts on genomic distance has been observed in all studied cell types [3][4][5] and can be utilized to infer the order of scaffolds in poorly assembled genomes, providing chromosome-length assemblies [6][7][8][9][10][11]. For species with a well-assembled genome, such as humans, the Hi-C technique can be used to detect structural variations, which alter the order of genomic segments and therefore lead to significant changes in chromatin interaction frequencies [6,[12][13][14][15][16][17]. In addition, one can extract information about single nucleotide variations (SNVs) from Hi-C reads.…”

Mechanisms of enhancer action: the known and the unknown

“…An enhancer and its cognate target gene almost always reside within a TAD; i.e., an enhancer’s functional jurisdiction is largely limited to the home TAD as it seldom contacts genes residing in neighboring TADs [ 232 , 233 ]. Sequence alterations at the TAD boundaries can restructure the adjacent TADs such that an enhancer can contact and activate a gene that resides in an otherwise inaccessible TAD, best illustrated in developmental disorders [ 234 , 235 ]. This spatial restriction eases the effort for the enhancer and cognate genes to find each other.…”

Interpreting the impact of noncoding structural variation in neurodevelopmental disorders

“…The deletion removes at least nine enhancer elements driving expression in the central nervous system (CNS). Recently, Melo et al identified a translocation disrupting the CTNNA2 TAD in a patient with ID and DD 116 . Although homozygous variants in this gene cause cortical dysplasia and other brain malformations, a noncoding disease mechanism has not yet been investigated.…”