3D position of pericentromeric heterochromatin within the nucleus of a patient with ICF syndrome

Abstract

ICF (immunodeficiency, centromeric region instability, facial anomalies) syndrome is a rare autosomal recessive disorder characterised by severe immunodeficiency, craniofacial anomalies and chromosome instability. Chromosome analyses from blood samples show a high frequency of decondensation of pericentromeric heterochromatin (PH) and rearrangements involving chromosomes 1 and 16. It is the first and, as far as we know, the only disease associated with a mutation in a DNA methyltransferase gene, DNMT3B, with significant hypomethylation of the classical satellite DNA, the major component of the juxtacentromeric heterochromatin. To better understand the complex links between the hypomethylation of the satellite DNA, the cytogenetic anomalies and the clinical features of ICF syndrome, we performed three-dimensional (3D) FISH on preserved cells from a patient with a suspected ICF phenotype. Analysis of DNMT3B did not reveal any mutation in our patient, making this case an ICF type 2. The results of 3D-FISH showed a statistically significant change in the intranuclear position of PH of chromosome 1 in cells of the patient as compared to normal cells. It is difficult to understand how a defect in the methylation pathway can be responsible for the various symptoms of this condition. From our observations we suggest a mechanistic link between the reorganisation of the nuclear architecture and the altered gene expression.

Three novel ZBTB24 mutations identified in Japanese and Cape Verdean type 2 ICF syndrome patients

“…P8: A 16-year-old Cape Verdean girl born in 1996 from nonconsanguineous parents. 18 She had characteristic facial features including epicanthic folds. She had recurrent thrush caused by candida infection in the first year of life.…”

“…Multibranched chromosomes were also observed. 18 DNA methylation status at satellites We examined the DNA methylation status of the satellite-2 and a-satellite repeats in the three ICF syndrome patients by Southern blot analysis using methylation-sensitive restriction enzymes. When satellite-2 was examined, the genomic DNAs from the three patients, as well as an ICF1 patient (P3), 19 gave multiple low-molecular-weight bands, indicating that this repeat was hypomethylated (Figure 2a).…”

3D-FISH analysis reveals chromatid cohesion defect during interphase in Roberts syndrome

“…The protocol was derived from Dupont et al . [ 16 ]. Air-drying of the preparation was carefully avoided in all experiments to preserve the 3D structure of nuclei.…”

“…Nuclear architecture and chromatin organization during interphase probably contributes to gene expression [ 9 ]. Abnormal spatial organization of the CTs in interphase was reported in tumor cells carrying chromosome translocations [ 12 ], in epilepsy [ 13 ], in laminopathies [ 14 ], and in ICF syndrome [ 15 , 16 ].…”

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

“…Fiber-FISH by locus-specific BAC clone probes within a 900 Kb 17q12 inversion hybridizing onto stretched DNA fibers correlated the inversion orientations with associated haplotypes, which allowed the evaluation of inversion frequencies among human populations globally (Donnelly et al, 2010). Pericentriomeric heterochromatin probes were used in a three dimensional FISH (3D-FISH) to study intra-nuclear centromeric positions in cultured cells from patients with ICF syndrome (immunodeficiency, centromeric region instability, facial anomalies) and Robert syndrome (cohesion defect by mutations in the ESCO2 gene) (Dupont et al, 2012, 2014). Multi-color FISH (M-FISH) by painting probes specific for a human chromosome and multi-color banding FISH (M-BAND) by painting probes specific for every band in a chromosome were used to visualize complex chromosomal rearrangements from chromothripsis in two patients with acute myeloid leukemia (Mackinnon and Campbell, 2013).…”