Analysis of nuclear scaffold/matrix attachment: The role of genome organization in transcription

The ordered packaging of DNA within the nucleus of somatic cells must be dynamic to support stable transcription interrupted by intermittent cycles of metaphase condensation. This dynamic packaging is intimately linked to the ability of DNA to complex with additional proteins, including both histones and non-histone proteins. Collectively, the non-histone proteins are termed the nuclear scaffold or nuclear matrix, depending on the method used to isolate them. Small scale studies have demonstrated that the regions of the genome that bind to the nuclear scaffold/matrix, also known as S/MARs, can also be differentiated from one another. However, these attachment regions are poorly defined at a global level that allows global functional characterization. To address this, the interactions between the genome and nuclear scaffold/matrix in multiple somatic human cell types as well as mature human spermatozoa have been characterized to define a transcriptional regulatory role for S/MARs on a genomic scale. Initial analysis in HeLa cells of both SARs and MARs revealed that they fulfill complementary roles in vivo. These differentially isolated regions work in concert to help mediate gene silencing (MARs) or to poise genes for expression (SARs). To define a role for cell-type specific attachment, SARs and MARs were then characterized in Aortic Adventitial Fibroblast (AoAF) cells. This analysis demonstrated that cell type specific DNA attachment to the nuclear scaffold/matrix can be used as a marker for facultatively expressed genes. The comparison of attachment and patterns of gene expression in the primary AoAF cells compared to that of HeLa S3 cells revealed a potential role for nuclear matrix mediated silencing in cellular division beyond Hayflick's limit. To determine if cells with silent genomes display global recruitment to the nuclear matrix, MARs were identified in mature human spermatozoa from individuals with proven fertility. This analysis revealed that the profile of nuclear matrix binding in sperm cells is significantly different than that of somatic cells with sites of marked enrichment appearing in only a few distinct, satellite repeat rich, regions of the genome. The differential organization suggests that widespread matrix attachment may be specifically involved in dynamic silencing as observed in cells with zones of transcription, such a the AoAF and HeLa cells. It is clear that the existing models suggesting sperm MAR spacing of approximately 25-50 kb, where individual toroids are attached to the nuclear matrix, should be reevaluated in light of these observations.