The “driver” represents a crucial part of a successful Formula One team, a decent score at golf, and even a well-planned bank heist (!), and working out those factors that drive the onset of various diseases and disorders may provide critical mechanistic insight and even aid the development of novel therapeutic approaches.
In the early-onset aging disease Hutchinson-Gilford progeria syndrome (HGPS), patients possess a mutant form of the nuclear envelope protein lamin A (known as progerin) that negatively impacts the inner nuclear membrane and prompts a range of cellular defects that induce early-onset aging. While epigenetic analysis has provided evidence for the alterations of histone methylation patterns and the loss of spatial compartmentalization of the typically observed active and inactive chromatin domains in patient-derived cells, the mechanism driving HGPS-associated epigenetic alterations remained unknown.
However, researchers led by Manuel Rodríguez-Paredes (DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany) knew that lamina-associated domains (or LADs), gene-poor DNA regions that lie close to the nuclear lamina and assist in the spatial organization of the genome into repressive elements, represented a leading contender. So, they maneuvered their research to ask whether disrupted LADs drive early-onset aging via the application of some hard-hitting epigenetic assays.
So, what did Köhler and their copilots discover about the role of LADs in driving HGPS-associated epigenetic alterations?
- ATAC-see provided a visual profile of chromatin accessibility
- While parental/age-matched control fibroblasts display a dynamic pattern of chromatin with both low and high accessibility regions, HGPS fibroblasts exhibit a reduction in chromatin accessibility accompanied by a nuclear malformation
- In agreement, ATAC-seq analysis identified 545 differentially accessible regions between HGPS and control fibroblasts that significantly overlap with LADs
- Methylome profiling by the EPIC array demonstrated that the altered DNA methylation profiles associate with LAD-specific chromatin accessibility changes
- Differential DNA methylation in HGPS fibroblasts primarily occurs at partially-methylated lamina-associated regions characterized by heterochromatic histone marks in normal dermal fibroblasts
- The DNA methylation alterations are distinct from those observed during healthy aging or in Werner syndrome, a progeroid syndrome caused by mutations to an ATP-dependent helicase
- Interestingly, HGPS samples form two subgroups based on DNA methylation profiles at the identified sites and age estimates from the epigenetic clock – an epigenetic age-accelerated group with higher levels of DNA methylation and a second group with a slight epigenetic age deceleration and lower DNA methylation
- RNA-seq identified 343 differentially expressed genes between HGPS and control fibroblasts, which are distinct from those observed during physiological aging
- Comparisons of transcriptomic, DNA methylation and chromatin accessibility datasets revealed a subset of the 343 differentially expressed genes that are directly affected by the epigenetic deregulation of LADs in HGPS
- Fluorescence in situ hybridization experiments in HGPS fibroblast nuclei revealed that overexpressed genes become repositioned away from the nuclear lamina, while downregulated genes relocate closer to the nuclear lamina
- This suggests that the intranuclear relocalization of lamina-associated loci underpins the aberrant gene expression patterns observed in HGPS fibroblasts
This multifactorial analysis now provides evidence that the progerin-driven nuclear malformation of HGPS nuclei leads to the epigenetic deregulation of LADs, which then drives the development of the disease-associated gene expression profile associated with the HGPS early-onset aging phenotype.
For more on the link between epigenetics, LADs, and early-onset aging syndromes, see Genome Medicine, May 2020.
If you’d like to read more about the ATAC-Seq method, please visit this great blog article from our friends at Active Motif – Complete Guide to Understanding and Using ATAC-Seq.