Tumor-associated aberrant silencing of CpG island-containing genes has been correlated with increased cytosine methylation, a "closed" chromatin structure, and exclusion of transcription factor binding in the CpG island/promoter regions of affected genes. Given the lack of understanding of what constitutes a closed chromatin structure in CpG islands, however, it has been difficult to assess the relationship among cytosine methylation, chromatin structure, and inappropriate gene silencing. In this study, nuclease accessibility analysis was used to more clearly define the chromatin structure in the CpG island of the human O 6 -methylguanine DNA methyltransferase (MGMT) gene. Chromatin structure was then related to in vivo DNA-protein interactions and cytosine methylation status of the MGMT CpG island in human glioma cells varying in MGMT expression. The results of these studies indicated that the "open" chromatin structure associated with the MGMT CpG island in MGMT ؉ cells consisted of an approximately 250-bp transcription factor-binding, nuclease-accessible, nucleosome-free region of DNA, whose formation was associated with at least four flanking, precisely positioned nucleosome-like structures. In MGMT ؊ cells, this precise nucleosomal array was lost and was replaced by randomly positioned nucleosomes (i.e., the closed chromatin structure), regardless of whether methylation of the CpG island was spread over the entire island or limited to regions outside the transcription factor binding region. These results suggest that CpG islands facilitate the expression of housekeeping genes by facilitating nucleosomal positioning and that the conditions that alter the formation of this array (such as perhaps methylation) may indirectly affect CpG island-containing gene expression.

GADD45 has been suggested to coordinate cell cycle regulation with the repair of DNA damage following ionizing radiation (IR). Although the GADD45 gene is transcriptionally up-regulated in response to IR, alterations in in vivo transcription factor (TF) binding or chromatin structure associated with up-regulation have not been defined. To understand how chromatin structure might influence TF binding and GADD45 up-regulation, key regulatory regions of the gene were identified by in vivo DNase I hypersensitivity (HS) analysis. Chromatin structure and in vivo TF binding in these regions were subsequently monitored in both non-irradiated and irradiated human ML-1 cells. In non-irradiated cells expressing basal levels of GADD45, the gene exhibited a highly organized chromatin structure with distinctly positioned nucleosomes. Also identified in non-irradiated cells were DNA-protein interactions at octamer binding motifs and a CCAAT box in the promoter and at consensus binding sites for AP-1 and p53 within intron 3. Upon irradiation and a subsequent 15-fold increase in GADD45 mRNA levels, neither the chromatin structure nor the pattern of TF binding in key regulatory regions was altered. These results suggest that the GADD45 gene is poised for up-regulation and can be rapidly induced independent of gross changes in chromatin structure or TF binding.

No abstract

Objective The purpose of this study was to determine whether new-onset transient postoperative atrial fibrillation (TPAF) affects mortality rates after abdominal aortic aneurysm (AAA) repair and to identify predictors for the development of TPAF. Methods Patients who underwent open aortic repair or endovascular aortic repair for a principal diagnosis AAA were retrospectively identified using the Healthcare Cost and Utilization Project-State Inpatient Database (Florida) for 2007 to 2011 and monitored longitudinally for 1 year. Inpatient and 1-year mortality rates were compared between those with and without TPAF. TPAF was defined as new-onset atrial fibrillation that developed in the postoperative period and subsequently resolved in patients without a history of atrial fibrillation. Cox proportional hazards models, adjusted for age, gender, comorbidities, rupture status, and repair method, were used to assess 1-year survival. Predictive models were built with preoperative patient factors using Chi-squared Automatic Interaction Detector decision trees and externally validated on patients from California. Results A 3.7% incidence of TPAF was identified among 15,148 patients who underwent AAA repair. The overall mortality rate was 4.3%. The inpatient mortality rate was 12.3% in patients with TPAF vs 4.0% in those without TPAF. In the ruptured setting, the difference in mortality was similar between groups (33.7% vs 39.9%, P = .3). After controlling for age, gender, comorbid disease severity, urgency (ruptured vs nonruptured), and repair method, TPAF was associated with increased 1-year postoperative mortality (hazard ratio, 1.48; P < .001) and postdischarge mortality (hazard ratio, 1.56; P = .028). Chi-squared Automatic Interaction Detector-based models (C statistic = 0.70) were integrated into a Web-based application to predict an individual's probability of developing TPAF at the point of care. Conclusions The development of TPAF is associated with an increased risk of mortality in patients undergoing repair of nonruptured AAA. Predictive modeling can be used to identify those patients at highest risk for developing TPAF and guide interventions to improve outcomes. (J Vasc Surg 2016;63:1240-7.)