|
| Status |
Public on Jan 11, 2023 |
| Title |
The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory (RNA-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Bi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to Immunodeficiency, Centromeric instability, Facial anomalies syndrome, type 1 (ICF1). While several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-induced pluripotent stem cells (iPSCs) and their CRISPR-Cas9 corrected clones to determine whether DNMT3B correction can globally overcome DNA methylation defects and related changes in the epigenome.
Hypomethylated regions throughout the genome were found highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1-peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are pre-marked during early development. CRISPR-corrected ICF1 iPSCs reveal that the majority of phenotype-related hypomethylated regions re-acquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increased H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persisted, and hypomethylation was uncorrected.
Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the ICF1 aberrant epigenome. However, a small fraction of the genome is resilient to this rescue, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.
|
| |
|
| Overall design |
In this study we examined the genome-wide DNA methylation level, gene expression, histone H3K4me3 and H3K36me3 marks enrichment, CTCF and DNMT3B binding in iPSCs derived from fibroblasts of healthy individuals, individuals affected by ICF syndrome type1 (ICF1 iPSCs) and ICF1 iPSCs corrected in the DNMT3B mutations following CRISPR/Cas9 editing.
|
| |
|
| Contributor(s) |
Poondi-Krishnan V, Morone B, Angelini C, Selig S, Matarazzo MR |
| Citation(s) |
36828588, 38136588 |
| |
| Submission date |
Mar 04, 2022 |
| Last update date |
Jan 02, 2024 |
| Contact name |
Maria Rosaria Matarazzo |
| Organization name |
Institute of Genetics and Biophysics "ABT"
|
| Street address |
Via Pietro Castellino 111
|
| City |
Napoli |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (19)
|
|
| This SubSeries is part of SuperSeries: |
| GSE197925 |
The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory |
|
| Relations |
| BioProject |
PRJNA812886 |
Less...
More...