On a molecular level, aging is associated with a gradual decline in the efficiency and accuracy of molecular processes, leading to a deterioration of cell functions including, but not limited to, global gene expression, DNA methylation, chromatin status and nuclear organization. Our previous data (see Nature 2014 for details) suggested that the association of subnuclear structures, such as the matrin-3-enriched nuclear network, with regulatory DNA elements is dynamic and is closely associated with the cell status. To study the importance of this association in aging and age-related diseases we developed novel technology – Matrix Associated DNA–sequencing (MAD-seq) which allows us to accurately and reproducibly map those associations and correlate with other genome-wide approaches, including global changes in transcription and 3D genome structure. Our approach gives us an unprecedented insight into the role of nuclear organization and its alterations during aging. This in turn will let us compare our epigenetic and transcriptomic data obtained in aging related eye diseases such as glaucoma and understand what component of the disease is strictly caused by deep global changes in nuclear structure and function.