Reactivation of maternal SNORD116 cluster via SETDB1 knockdown in Prader-Willi syndrome iPSCs

Area of Science:

• Epigenetics
• Genomic imprinting
• Molecular biology

Background:

• Prader-Willi syndrome (PWS) is a genetic disorder caused by the loss of paternal gene copies on chromosome 15q11-q13.
• This region contains the SNORD116 C/D box snoRNAs and their host transcript, 116HG, which are subject to genomic imprinting.

Purpose of the Study:

• To investigate the epigenetic mechanisms responsible for repressing the maternal SNORD116 cluster and 116HG in Prader-Willi syndrome.
• To identify the protein complex involved in silencing the maternal 15q11-q13 region.

Main Methods:

• Utilized PWS-specific induced pluripotent cells (iPSCs).
• Performed knockdown of SETDB1 (a histone methyltransferase) to observe effects on chromatin marks and gene expression.
• Analyzed DNA methylation patterns at the PWS imprinting control center (PWS-IC).

Main Results:

• Identified a ZNF274/SETDB1 complex that binds to the silent maternal, but not the active paternal, alleles of SNORD116/116HG.
• SETDB1 knockdown decreased H3K9 trimethylation (H3K9me3) and increased H3K4 dimethylation (H3K4me2) at 116HG.
• SETDB1 knockdown partially restored maternal 116HG RNA expression and disrupted DNA methylation at the PWS-IC, decreasing 5-methylcytosine and increasing 5-hydroxymethylcytosine.

Conclusions:

• The ZNF274/SETDB1 complex plays a crucial role in repressing maternal gene expression in the 15q11-q13 region.
• This complex may protect the PWS-IC from DNA demethylation during early development.
• Findings reveal novel epigenetic mechanisms underlying Prader-Willi syndrome pathogenesis.