Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function

<jats:title>Summary</jats:title><jats:p>Topologically associating domain (TAD) boundaries are thought to partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotype<jats:sup>1–3</jats:sup>, but the overall extent to which this occurs remains unknown. Here we show that TAD boundary deletions commonly disrupt normal genome function<jats:italic>in vivo</jats:italic>. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80kb in size) from the genome in mice. All deletions examined resulted in at least one detectable molecular or organismal phenotype, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. For 5 of 8 (62%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near<jats:italic>Smad3/Smad6</jats:italic>caused complete embryonic lethality, while a deletion near<jats:italic>Tbx5/Lhx5</jats:italic>resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for<jats:italic>in vivo</jats:italic>genome function and suggest that noncoding deletions affecting TAD boundaries should be carefully considered for potential pathogenicity in clinical genetics screening.</jats:p>