Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity

Abstract

DNA loop organization by nuclear scaffold/matrix attachment is a key regulator of gene expression that may provide a means to modulate phenotype. We have previously shown that attachment of genes to the NaCl-isolated nuclear matrix correlates with their silencing in HeLa cells. In contrast, expressed genes were associated with the lithium 3,5-diiodosalicylate (LIS)-isolated nuclear scaffold. To define their role in determining phenotype matrix attached regions (MARs) on human chromosomes 14–18 were identified as a function of expression in a primary cell line. The locations of MARs in aortic adventitial fibroblast (AoAF) cells were very stable (r = 0.909) and 96% of genes attached at MARs are silent (P < 0.001). Approximately one-third of the genes uniquely expressed in AoAF cells were associated with the HeLa cell nuclear matrix and silenced. Comparatively, 81% were associated with the AoAF cell nuclear scaffold (P < 0.001) and expressed. This suggests that nuclear scaffold/matrix association mediates a portion of cell type-specific gene expression thereby modulating phenotype. Interestingly, nuclear matrix attachment and thus silencing of specific genes that regulate proliferation and maintain the integrity of the HeLa cell genome suggests that transformation may at least in part be achieved through aberrant nuclear matrix attachment.

Loop domain organization of the p53 locus in normal and breast cancer cells correlates with the transcriptional status of the TP53 and the neighboring genes

“…The small number of attachment sites observed in the studied 167 kb region comprising the TP53 gene locus is in agreement with the previous study of Linnemann and Krawetz [2009b]. They have shown, by screening human chromosomes 14-18, a correlation between high gene density and low number of MARs.…”

The sperm nucleus: chromatin, RNA, and the nuclear matrix

“…A subset of sperm RNAs may also serve to structurally support the nuclear matrix (Linnemann 2009). This proteinaceous network present in most cells functionally organizes the genome by binding discreet regions of DNA at sequences termed Scaffold/Matrix Attachment Regions (S/MARs).…”

Nuclear Matrix Association: Switching to the Invasive Cytotrophoblast

“…Comparison of p53 expressing and p53 null tumors has revealed that the loss of this nuclear matrix binding protein allows a cell to escape from the normal G1 arrest of the cell cycle during which DNA damage is repaired[47]. This loss of binding to the nuclear matrix may disrupt the normal local looping patterns and expose origins of replication or result in the loss of nuclear matrix associated gene silencing [30]. In turn, this would likely result in the aberrant expression of proteins that allow progression through the cell cycle.…”

“…Both HTR-F and HTR-M, matrix and loop DNA were isolated after optimal extraction as described [29] [30]. Briefly, the halo structures were gently washed with REact® 3 restriction buffer (Invitrogen, Carlsbad, CA, USA) for 20 minutes at room temperature then centrifuged at 1000 × g at 4°C.…”

“…Methods previously detailed [27, 30] were used to evaluate the dataset and to identify a parsimonious sets of MARs found in both cell types and unique to either cell type. Briefly, the sites of significance were identified if the putative MAR fulfilled three criteria.…”