Characterization of Higher-order Chromatin Structure in Bone Differentiation and Breast Cancer: A Dissertation

Higher-order genome organization is important for the regulation of gene expression by bringing different cis-regulatory elements and promoters in proximity. The establishment and maintenance of long-range chromatin interactions occur in response to cellular and environmental cues with the binding of transcription factors and chromatin modifiers. Understanding the organization of the nucleus in differentiation and cancer has been a long standing challenge and is still not well-understood. In this thesis, I explore the dynamic changes in the higher-order chromatin structure in bone differentiation and breast cancer. First, we show dynamic chromatin contact between a distal regulatory element and the promoter of Runx2 gene, which encodes the Runtrelated transcription factor 2 (RUNX2) that is essential for bone development. Next, via using a genome-wide approach, we show that breast cancer cells have altered long-range chromatin contacts among small, gene-rich chromosomes and at telomeres when compared with mammary epithelial cells. Furthermore, we assess the changes in nuclear structure and gene expression of breast cancer cells following Runt-related transcription factor 1 (RUNX1) deficiency, an event frequently observed in breast cancer. Finally, I present the role of the central ATPase subunit of the SWI/SNF complex, SMARCA4 (BRG1), in mediating nuclear structure and gene expression. Taken together, the research presented in this thesis reveals novel insight and paradigm for the dynamic changes in disease and differentiation, as well as uncovers previously unidentified roles for two chromatin regulatory proteins, RUNX1 and SMARCA4

Bidirectional tachycardia in a patient with pulmonary embolism

We report a 55 year-old man with sudden cardiac arrest. Electrocardiography revealed runs of bidirectional ventricular tachycardia, and transthoracic echocardiography showed indirect findings of pulmonary embolism. (Cardiol J 2010; 17, 2: 194-195

The connection between BRG1, CTCF and topoisomerases at TAD boundaries

The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries. In this review, we elaborate on our findings and speculate that BRG1 may contribute to the regulation of the structural and functional properties of chromatin at TAD boundaries by affecting the function or the recruitment of CTCF and DNA topoisomerase complexes

Cancer-testis gene expression is associated with the methylenetetrahydrofolate reductase 677 C\u3eT polymorphism in non-small cell lung carcinoma

BACKGROUND: Tumor-specific, coordinate expression of cancer-testis (CT) genes, mapping to the X chromosome, is observed in more than 60% of non-small cell lung cancer (NSCLC) patients. Although CT gene expression has been unequivocally related to DNA demethylation of promoter regions, the underlying mechanism leading to loss of promoter methylation remains elusive. Polymorphisms of enzymes within the 1-carbon pathway have been shown to affect S-adenosyl methionine (SAM) production, which is the sole methyl donor in the cell. Allelic variants of several enzymes within this pathway have been associated with altered SAM levels either directly, or indirectly as reflected by altered levels of SAH and Homocysteine levels, and altered levels of DNA methylation. We, therefore, asked whether the five most commonly occurring polymorphisms in four of the enzymes in the 1-carbon pathway associated with CT gene expression status in patients with NSCLC. METHODS: Fifty patients among a cohort of 763 with NSCLC were selected based on CT gene expression status and typed for five polymorphisms in four genes known to affect SAM generation by allele specific q-PCR and RFLP. RESULTS: We identified a significant association between CT gene expression and the MTHFR 677 CC genotype, as well as the C allele of the SNP, in this cohort of patients. Multivariate analysis revealed that the genotype and allele strongly associate with CT gene expression, independent of potential confounders. CONCLUSIONS: Although CT gene expression is associated with DNA demethylation, in NSCLC, our data suggests this is unlikely to be the result of decreased MTHFR function

Epigenetic control of cell cycle-dependent histone gene expression is a principal component of the abbreviated pluripotent cell cycle

Self-renewal of human pluripotent embryonic stem cells proceeds via an abbreviated cell cycle with a shortened G(1) phase. We examined which genes are modulated in this abbreviated period and the epigenetic mechanisms that control their expression. Accelerated upregulation of genes encoding histone proteins that support DNA replication is the most prominent gene regulatory program at the G(1)/S-phase transition in pluripotent cells. Expedited expression of histone genes is mediated by a unique chromatin architecture reflected by major nuclease hypersensitive sites, atypical distribution of epigenetic histone marks, and a region devoid of histone octamers. We observed remarkable differences in chromatin structure--hypersensitivity and histone protein modifications--between human embryonic stem (hES) and normal diploid cells. Cell cycle-dependent transcription factor binding permits dynamic three-dimensional interactions between transcript initiating and processing factors at 5\u27 and 3\u27 regions of the gene. Thus, progression through the abbreviated G(1) phase involves cell cycle stage-specific chromatin-remodeling events and rapid assembly of subnuclear microenvironments that activate histone gene transcription to promote nucleosomal packaging of newly replicated DNA during stem cell renewal

Cancer-testis gene expression is associated with the methylenetetrahydrofolate reductase 677 C>T polymorphism in non-small cell lung carcinoma

Background: Tumor-specific, coordinate expression of cancer-testis (CT) genes, mapping to the X chromosome, is observed in more than 60% of non-small cell lung cancer (NSCLC) patients. Although CT gene expression has been unequivocally related to DNA demethylation of promoter regions, the underlying mechanism leading to loss of promoter methylation remains elusive. Polymorphisms of enzymes within the 1-carbon pathway have been shown to affect S-adenosyl methionine (SAM) production, which is the sole methyl donor in the cell. Allelic variants of several enzymes within this pathway have been associated with altered SAM levels either directly, or indirectly as reflected by altered levels of SAH and Homocysteine levels, and altered levels of DNA methylation. We, therefore, asked whether the five most commonly occurring polymorphisms in four of the enzymes in the 1-carbon pathway associated with CT gene expression status in patients with NSCLC.Publisher's Versio

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

BACKGROUND: Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines. RESULTS: Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16-22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16-22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells. CONCLUSIONS: We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer

Okul yöneticilerinin sergiledikleri takım liderliği davranışları ile öğretmen motivasyonları arasındaki ilişki

Bu çalışmanın amacı, ilkokul ve ortaokul öğretmenlerinin algılarına göre okul yöneticilerinin takım liderliği davranışları ile öğretmenlerin motivasyonları arasındaki ilişkiyi incelemektir. Tarama modelinde yürütülen bu araştırmanın örneklemi, Denizli İli Çivril ilçesindeki ilköğretim ve ortaöğretim okullarında görev yapan 217 öğretmenden oluşmaktadır. Araştırma için gerekli verileri,“Takım Liderliği Ölçeği” ve “Öğretmen Motivasyon Ölçeği” aracılığıyla toplanmıştır. Araştırmada elde edilen verilerin analizinde öncelikle öğretmenlerin yöneticilerinin takım liderliği davranışlarını ve motivasyon düzeylerini belirlemeye yönelik betimsel istatistik değerleri(aritmetik ortalama, standart sapma) hesaplanmış, demografik değişkenlerine ilişkin karşılaştırmalarda da t-testi ve tek yönlü varyans analizi kullanılmıştır. Ayrıca takım liderliği davranışları ile motivasyon düzeyleri arasındaki ilişkiyi belirlemek için Pearson Çarpım Moment Korelasyon analizinden yararlanılmıştır. Araştırmada elde edilen bulgular doğrultusunda öğretmenlerin yöneticilerinin takım liderliği davranışlarını sergilediklerini düşündükleri ve motivasyon düzeylerinin de yüksek olduğu sonucuna ulaşılmıştır. Bunun yanı sıra, okul yöneticilerinin takım liderliği davranışlarını sergilemeleri ile öğretmenlerin motivasyon düzeyleri arasında bir ilişkinin olduğu sonucuna ulaşılmıştır

EVALUATION OF SURFACE ECG CHANGES IN PREGNANT WOMEN WITH GESTATIONAL DIABETES MELLITUS

Objective: Gestational diabetes mellitus (GDM) has an increased risk of maternal and fetal complications. Increased maternal cardiac risk is one of the most important complications. QT dispersion and Tp-e duration are findings of surface electrocardiogram (ECG) and they are used an index of inhomogeneity in ventricular electrical activity, and prolongation of QT dispersion is related to increased incidence of ventricular arrhythmias. In this study, we aimed to investigate QT dispersion, Tp-e interval and Tp-eIQT ratio in pregnant women with GDM and emphasize the increased cardiac risk and the importance of GDM screenin