Wilson et al. (IJMS, 2021) review on CHD2-related CNS pathologies

Q1. What are the four major families of chromatin remodelers based on structural differences?

SWI/SNF (switch/sucrose non-fermenting), ISWI (imitation switch), INO80 (inositol 80), and CHD (chromodomain helicase DNA binding).

Q2. What uniquely distinguishes CHD family proteins from other chromatin remodelers?

They uniquely possess a pair of tandem chromodomains (chromatin organization modifier domains) in addition to the SNF2-like ATPase/helicase domain.

Q3. How are the nine human CHD proteins divided into subfamilies?

Subfamily I: CHD1 and CHD2 (have C-terminal DNA binding domain); Subfamily II: CHD3, CHD4, CHD5 (have two PHD zinc finger domains); Subfamily III: CHD6, CHD7, CHD8, CHD9 (structurally variable, often have BRK domains).

Q4. What epigenetic mark do CHD1 and CHD2 recognize via their tandem chromodomains?

H3K4me2/3 (histone H3 lysine 4 di- and tri-methylation), which is associated with transcriptionally active euchromatin.

Q5. What is the canonical function of CHD proteins?

Spatial and temporal regulation of gene expression via reversible structural and chemical changes to DNA, modulating accessibility of the transcriptional machinery.

Q6. What human developmental epileptic encephalopathy is caused by mutations in CHD2?

CHD2-related developmental epileptic encephalopathy (CHD2-DEE), characterized by early-onset seizures (often myoclonic), cognitive regression, intellectual disability, and often autism spectrum disorder-like behaviors.

Q7. At what age do seizures typically begin in CHD2-DEE patients, and what are common seizure types?

Usually as early as 6 months old and generally before 4 years of age; seizure types include myoclonus, myoclonic-absence seizures, and drop attacks; photosensitivity is often present.

Q8. What is the genetic basis of CHD2-DEE?

De novo loss-of-function mutations (including hemizygous deletions) in the CHD2 gene on chromosome 15q26.1, leading to haploinsufficiency.

Q9. What phenotypic overlap exists between CHD2-DEE and Dravet syndrome?

Both share sensitivity to fever-induced seizures, intellectual disability; about one-third of Dravet patients without SCN1A mutations were found to harbor CHD2 mutations.

Q10. What did the Chd2 knockdown zebrafish model reveal about seizures and photosensitivity?

Chd2 knockdown larvae displayed abnormal movements, seizure-like epileptiform discharges, and markedly increased photosensitivity (abnormal cortical response to flickering light).

Q11. What are the phenotypes of CHD2 heterozygous (Chd2+/-) mouse models?

Perinatal lethality (some lines), growth retardation, lordokypnosis, lowered body fat, postnatal runting, cognitive and long-term memory deficits, aberrant DNA damage repair, and increased susceptibility to lymphomas.

Q12. Why are Chd2 homozygous knockout mice non-viable?

Homozygous mutants display perinatal lethality and developmental abnormalities prior to death.

Q13. What biochemical activities of CHD2 have been characterized in vitro?

CHD2 assembles regularly spaced nucleosome arrays from purified components in the presence of ATP (functions as a chromatin assembly factor) and has ATP-dependent chromatin remodeling activity.

Q14. What role does CHD2 play in DNA repair?

PARP1 recruits CHD2 to sites of DNA double-strand breaks; CHD2 expands chromatin and deposits H3.3 histone variants to initiate non-homologous end joining (NHEJ) repair.

Q15. How does CHD2 regulate the REST gene (Neuron-Restrictive Silencer Factor)?

CHD2 binds directly to the REST gene; when CHD2 is silenced, REST expression decreases; when CHD2 is overexpressed, REST expression increases. This occurs via direct association, not mediated by H3K4me.

Q16. What is the long non-coding RNA that regulates CHD2 expression in cis, and what happens when it is lost?

Chaserr (CHD2 Adjacent Suppressive Regulatory RNA, also known as LINC01578); loss of Chaserr leads to increased CHD2 expression, and the phenotypic consequences are rescued when CHD2 is also perturbed.

Q17. How does CHD2 interact with the interneuron development transcription factor NKX2-1?

CHD2 regulates cortical interneuron (cIN) development via interaction with the medial ganglionic eminence (MGE)-associated transcription factor NKX2-1.

Q18. What is the role of CHD2 in myogenic differentiation?

CHD2 was identified as a regulator of MyoD (a transcription factor that determines cell fate); CHD2 incorporates the histone variant H3.3 into genes in cells destined to differentiate into muscle cells.

Q19. Name three other human diseases associated with mutations in CHD family proteins besides CHD2-DEE.

CHARGE syndrome (CHD7), autism spectrum disorder (CHD8), Sifrim-Hitz-Weiss syndrome (CHD4), neuroblastoma (CHD5), dermatomyositis (CHD3/CHD4), prostate cancer (CHD1).

Q20. What is the proposed advantage of using iPSC-derived neurons or brain organoids for studying CHD2 mutations?

Allows modeling of specific patient mutations in human cells; CRISPR/Cas9 base editing can introduce precise mutations; provides access to human-specific developmental mechanisms not recapitulated in animal mode