3. How is chromatin structure dysregulated in disease

What are structural variants (SVs)?

Structural and quantitative chromosomal rearrangements [answer] Structural variants are structural and quantitative chromosomal rearrangements that contribute to genetic diversity and are relevant for cancer genetics, rare diseases, and evolutionary genetics.

How can SVs affect gene expression?

By altering copy number of regulatory elements or disrupting higher-order chromatin organisation [answer] SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher-order chromatin organisation such as TADs.

What is a fused TAD?

A TAD caused by deletion of a TAD boundary [answer] Fused TADs can be caused by deletion of a TAD boundary (CTCF binding site), merging two adjacent TADs into one.

What is a neo-TAD?

A new TAD formed by duplication of a genomic region including a TAD boundary [answer] Neo-TADs can be caused by duplication of a genomic region including a TAD boundary (CTCF binding site), creating a new chromatin domain.

What is a shuffled TAD?

A TAD caused by inversion of a genomic region [answer] Shuffled TADs can be caused by inversion of a genomic region altering the presence of enhancers or other regulatory elements in the involved TADs.

What is enhancer adoption?

Relocation of enhancer elements into a neighbouring TAD causing misexpression [answer] Enhancer adoption occurs when a deletion of a boundary allows an enhancer from one TAD to act on a gene in a neighbouring TAD, driving ectopic expression.

What syndrome is associated with duplications of enhancer elements at the IHH locus?

Synpolydactyly [answer] Duplications of enhancer elements at the IHH locus within TADs cause tissue-specific misregulation of IHH expression, associated with synpolydactyly (fusion of digits and supernumerary digits).

What is Cooks syndrome and what causes it?

Short digits and nail aplasia caused by duplication of a TAD boundary at the SOX9 locus [answer] Cooks syndrome is characterised by short digits and nail aplasia, caused by duplication of a TAD boundary at the SOX9 locus leading to neo-TAD formation.

What did the Ibrahim lab show by removing CTCF binding motifs between Kcnj2-TAD and Sox9-TAD?

Formation of a larger fused TAD and altered gene expression patterns [answer] Removal of CTCF binding motifs led to the formation of a larger fused TAD, with Sox9 expression no longer limited to the digits and Kcnj2 expression found de novo in the digits.

What disease is associated with deletion of a TAD boundary at the LMNB1 locus?

Adult-onset demyelinating leukodystrophy [answer] Deletion of a TAD boundary at the LMNB1 locus causes enhancer adoption and adult-onset demyelinating leukodystrophy.

What is F syndrome and what causes it?

Syndactyly of thumb and index finger caused by inversions at the EPHA4 locus [answer] Inversions of an enhancer cluster at the EPHA4 locus cause enhancer adoption and misregulation of WNT6, associated with F syndrome (syndactyly of thumb and index finger).

What are chromatinopathies?

Disorders caused by mutations in chromatin regulators [answer] Chromatinopathies are neurodevelopmental disorders that arise from mutations in genes at various levels of chromatin organisation. Over 100 have been reported to date.

What is Cornelia de Lange Syndrome (CdLS)?

A multisystem developmental disorder caused by mutations in cohesin complex subunits [answer] CdLS is characterised by facial dysmorphisms, upper limb abnormalities, growth delay, and cognitive retardation. It was first described in 1918.

Which genes are mutated in Cornelia de Lange Syndrome?

NIPBL (~65%), SMC1A, SMC3, and RAD21 [answer] CdLS is caused by mutations in NIPBL (the majority, ~65%), SMC1A (X-linked recessive), SMC3, and RAD21 - all components of the cohesin complex.

What is the function of NIPBL?

Loading the cohesin ring onto chromatin [answer] NIPBL and MAU2 subunits are crucial for loading the Cohesin ring onto chromatin.

What happens in RAD21 mutations causing CdLS?

Missense mutations cluster at the interface with STAG2 and SMC1A, impairing DNA damage response [answer] RAD21 mutations act at the interface with STAG2 and SMC1A, impair cellular DNA damage response, and disrupt transcription. Dominant missense mutations cause more severe functional defects than loss-of-function mutations.

How does SMC1A cause CdLS?

Through X-linked recessive inheritance [answer] SMC1A mutations are responsible for CdLS through X-linked recessive inheritance, affecting male members of affected families.

What happens to TAD structure when CTCF binding sites are deleted at the SOX9-Kcnj2 locus?

Formation of a larger fused TAD [answer] Deletion of CTCF binding sites between the Kcnj2-TAD and Sox9-TAD leads to the formation of a larger fused TAD, mimicking the molecular genetics of Cooks syndrome.

How do structural variants create specific signatures in Hi-C maps?

They produce ectopic interactions visible in interaction maps [answer] Structural variants create specific signatures noticeable by visual inspection of Hi-C interaction maps, including TAD fusion (deletion), neo-TAD formation (duplication), or TAD shuffling (inversi