Topologically associating domain boundaries are required for normal genome function

Abstract

Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1–3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11–80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.

Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture

“…In the genome of mammals and teleost fish, SMAD3 and SMAD6 locate closely together, but in different topologically associated domains 16 . Since zebrafish express smad3a, smad3b, smad6a and smad6b [51][52][53][54] , this model provides flexibility to investigate the interactions between these genes upon gene dosage.…”

“…Interestingly, identical pathogenic variants in SMAD6 may result in either cardiovascular anomalies, craniosynostosis or radioulnar synostosis 13 . Because SMAD3 and SMAD6 have been in linkage disequilibrium throughout evolution from teleost fish to human, it has been postulated that SMAD3 could have a modifier role on SMAD6 deficiency 16 . In line with this observation, we identified a 1.5 Mb 15q22.31-15q23 microdeletion encompassing SMAD3 and SMAD6 in an 11-year-old-boy and his 33-year-old mother, both presenting with bicuspid aortic valve and arterial tortuosity, but no aneurysms, along with skeletal and cutaneous anomalies of LDS3, hinting that deletion of SMAD6 may influence the phenotype caused by SMAD3 LOF ( Supplementary Case Presentation 17 ).…”

A comprehensive catalog of 3D genome organization in diverse human genomes facilitates understanding of the impact of structural variation on chromatin structure

“…Our findings have critical implications for understanding human whole-genome sequencing data in disease diagnosis and precision medicine. Genomic variation, including all types of SVs that overlap or intersect with TAD boundaries in human genomes, should be further investigated to better understand the molecular basis of human genetic diseases 26 .…”

Novel Missing Data Imputation Approaches Enhance Quantitative Trait Loci Discovery in Multi-Omics Analysis

“…Following basic processing procedures (elaborated in Figure 1), we select subsets of molecular features for proteomics and metabolomics data requiring that 1) features have no missing entry for MCAR based simulation scenarios; 2) features with less than 5% missing rate in the MNAR scenario. For methylation data containing many CpG sites, we compute PCA of CpGs in each topologically associating domain (TAD) [39] and select up to 10 CpG most correlated to the first PC with R 2 > 0.75.…”