Genomic imprinting in mammals: an interplay between chromatin and DNA methylation?

Most imprinted loci have key regulatory elements that are methylated on only one of the parental chromosomes. For several of these 'differentially methylated regions', recent studies establish that the unmethylated chromosome has a specialized chromatin organization that is characterized by nuclease hypersensitivity. The novel data raise the question of whether specific proteins and associated chromatin features regulate the allele-specificity of DNA methylation at these imprinting control elements.     

Oxygen levels and the regulation of cell adhesion in the nervous system: A control point for morphogenesis in development,disease and evolution?

In this article, I discuss the hallmarks of hypoxia in vitro and in vivo and review work showing that many types of stem cell proliferate more robustly in lowered oxygen. I then discuss recent studies showing that alterations in the levels and the types of cell and substrate adhesion molecules are a notable response to reduced O₂ levels in both cultured primary neural stem cells and brain tissues in response to hypoxia in vivo. The ability of O₂ levels to regulate adhesion molecule expression is linked to the Wnt signaling pathway, which can control and be controlled by adhesion events. The ability of O₂ levels to influence cell adhesion also has far-reaching implications for development, ischemic trauma and neural regeneration, as well as for cancer and other diseases. Finally I discuss the possibility that the fluctuations in O₂ levels known to have occurred over evolutionary time could, by influencing adhesion systems, have contributed to early symbiotic events in unicellular organisms and to the emergence of multicellularity. It is not my intention to be exhaustive in these domains, which are far from my own field of study. Rather this article is meant to provoke and stimulate thinking about molecular evolution involving O₂ sensing and signaling during eras of geologic and atmospheric change that might inform modern studies on development and disease.     

Parental epigenetic control of embryogenesis: a balance between inheritance and reprogramming?

At fertilization, fusion of two differentiated gametes forms the zygote that is capable of forming all of the varied cell lineages of an organism. It is widely thought that the acquisition of totipotency involves extensive epigenetic reprogramming of the germline state into an embryonic state. However, recent data argue that this reprogramming is incomplete and that substantial epigenetic information passes from one generation to the next. In this review we summarize the changes in chromatin states that take place during mammalian gametogenesis and examine the evidence that early mammalian embryogenesis may be affected by inheritance of epigenetic information from the parental generation.     

Association of cigarette smoking and CRP levels with DNA methylation in α-1 antitrypsin deficiency

Alpha-1 antitrypsin (AAT) deficiency and tobacco smoking are confirmed risk factors for Chronic Obstructive Pulmonary Disease. We hypothesized that variable DNA methylation would be associated with smoking and inflammation, as reflected by the level of C-Reactive Protein (CRP) in AAT-deficient subjects. Methylation levels of 1,411 autosomal CpG sites from the Illumina GoldenGate Methylation Cancer Panel I were analyzed in 316 subjects. Associations of five smoking behaviors and CRP levels with individual CpG sites and average methylation levels were assessed using non-parametric testing, linear regression and linear mixed effect models, with and without adjustment for age and gender. Univariate linear regression analysis revealed that methylation levels of 16 CpG sites significantly associated with ever-smoking status. A CpG site in the TGFBI gene was the only site associated with ever-smoking after adjustment for age and gender. No highly significant associations existed between age at smoking initiation, pack-years smoked, duration of smoking, and time since quitting smoking as predictors of individual CpG site methylation levels. However, ever-smoking and younger age at smoking initiation associated with lower methylation level averaged across all sites. DNA methylation at CpG sites in the RUNX3, JAK3 and KRT1 genes associated with CRP levels. The most significantly associated CpG sites with gender and age mapped to the CASP6 and FZD9 genes, respectively. In summary, this study identified multiple potential candidate CpG sites associated with ever-smoking and CRP level in AAT-deficient subjects. Phenotypic variability in Mendelian diseases may be due to epigenetic factors.     

α-Satellite DNA methylation in normal individuals and in ICF patients: heterogeneous methylation of constitutive heterochromatin in adult and fetal tissues

The methylation profile of ten α-satellites was investigated in normal individuals and in ICF (Immunodeficiency, Centromeric instability, Facial abnormalities) patients. Two out of three ICF patients showed modified methylation of these sequences, reproducing a placental profile. CENP-B boxes, the binding sites of centromeric protein B, were always skewed toward nonmethylation. Unexpected results were observed in normal individuals: in somatic adult tissues the methylation pattern of α-satellite DNA varied between chromosomes, and in fetal tissues these satellites were homogeneously undermethylated. Detailed methylation analysis of CENP-B boxes revealed that unmethylated α-satellite units coexist with thoroughly methylated regions. These observations showed that the two major components of constitutive heterochromatin are differently methylated in normal somatic and fetal tissues, since classical satellites are consistently methylated. The definite changes in the methylation profile of heterochromatin in somatic chromosomes and the asynchronous timing of methylation of classical and α-satellites during development may reflect specific roles of highly repeated sequences in genomic organization. Received: 29 October 1996 / Revised: 17 December 1996     

The state of DNA methylation of human ϵ-globin gene in erythroid and non-erythroid cells

The extent of DNA methylation within the embryonic human ϵ-globin gene domain was studied in erythroid and non-erythroid cell lines. The results obtained show that the human ϵ-globin gene is totally methylated at all sites tested in tissues where it is not expressed, i.e. blood leucocytes. In the erythroid cell lines, K562 and PUTKO, both forced to embryonic differentiation by induction with haemin, the level of methylation is reduced compared with that observed in blood leucocytes. In the nonerythroid cell lines HeLa and Raji, where the human ϵ-globin gene is not expressed, the overall level of methylation in all sites tested is lower compared with that in erythroid cell lines.     

Epigenetic inheritance and genome regulation: is DNA methylation linked to ploidy in haplodiploid insects?

Organisms show great variation in ploidy level. For example, chromosome copy number varies among cells, individuals and species. One particularly widespread example of ploidy variation is found in haplodiploid taxa, wherein males are typically haploid and females are typically diploid. Despite the prevalence of haplodiploidy, the regulatory consequences of having separate haploid and diploid genomes are poorly understood. In particular, it remains unknown whether epigenetic mechanisms contribute to regulatory compensation for genome dosage. To gain greater insights into the importance of epigenetic information to ploidy compensation, we examined DNA methylation differences among diploid queen, diploid worker, haploid male and diploid male Solenopsis invicta fire ants. Surprisingly, we found that morphologically dissimilar diploid males, queens and workers were more similar to one another in terms of DNA methylation than were morphologically similar haploid and diploid males. Moreover, methylation level was positively associated with gene expression for genes that were differentially methylated in haploid and diploid castes. These data demonstrate that intragenic DNA methylation levels differ among individuals of distinct ploidy and are positively associated with levels of gene expression. Thus, these results suggest that epigenetic information may be linked to ploidy compensation in haplodiploid insects. Overall, this study suggests that epigenetic mechanisms may be important to maintaining appropriate patterns of gene regulation in biological systems that differ in genome copy number.     

Lepidopteran cells,an alternative for the production of recombinant antibodies?

Monoclonal antibodies are used with great success in many different therapeutic domains. In order to satisfy the growing demand and to lower the production cost of these molecules, many alternative systems have been explored. Among them, the baculovirus/insect cells system is a good candidate. This system is very safe, given that the baculoviruses have a highly restricted host range and they are not pathogenic to vertebrates or plants. But the major asset is the speed with which it is possible to obtain very stable recombinant viruses capable of producing fully active proteins whose glycosylation pattern can be modulated to make it similar to the human one. These features could ultimately make the difference by enabling the production of antibodies with very low costs. However, efforts are still needed, in particular to increase production rates and thus make this system commercially viable for the production of these therapeutic agents.     

Global DNA methylation profile at LINE-1 repeats and promoter methylation of genes involved in DNA damage response and repair pathways in human peripheral blood mononuclear cells in response to γ-radiation

Molecular and Cellular Biochemistry - DNA methylation is an epigenetic mechanism, which plays an important role in gene regulation. The present study evaluated DNA methylation profile of LINE1...     

Shh Signaling and Pancreatic Cancer: Implications for Therapy?

Hedgehog signaling has been implicated in the development of several human cancers, including small cell lung carcinomas, medulloblastomas, basal cell carcinomas, and digestive tract tumors. Elevated levels of pathway components are observed in pancreatic ductal adenocarcinoma (PDAC) precursor lesions, and these levels increase further as lesions progress to more advanced stages. Yet the mechanisms by which hedgehog signaling contributes to pancreatic tumorigenesis were poorly understood. We recently published results showing that activated hedgehog signaling enhances the proliferation and survival of pancreatic duct epithelial cells, the presumptive target cells for PDAC development. We also demonstrated that sonic hedgehog (Shh) expression, in cooperation with loss of the Trp53 and Ink4a/Arf tumor suppressor loci, was sufficient to initiate the formation of early pancreatic lesions. Furthermore, Shh signaling enhanced K-Ras-mediated pancreatic tumorigenesis and reduced the dependence of tumor cells on the sustained activation of Ras-stimulated signaling pathways. Here we discuss the significance of these findings and the implications for therapy.     

Genetic and epigenetic alterations in breast cancer: what are the perspectives for clinical practice?

The worldwide incidence of breast cancer affects 1.2 million women each year. In contrast to the high occurrence of this malady, a decline in mortality is reported among industrialized countries. In this respect, both awareness campaigns and substantial progress achieved in therapy and diagnosis allowed for the enhancement of the survival rate in patients with breast cancer. Undoubtedly, oncology research programs played a relevant role in the improvement of therapeutics and diagnostics for breast cancer. Major strides were reported, especially over the last decade and a half, in better understanding molecular and cellular biology events involved in breast cancer pathogenesis and progression of the disease. However, therapeutic approaches for the treatment of patients with breast cancer need further improvement. Therapeutic interventions can chronically compromise both the state of health and quality of life of breast cancer survivors. In addition, current therapeutic approaches have not significantly improved the survival rate in patients with metastatic disease. On these grounds, it is necessary to develop more efficient therapeutics and diagnostic tools, which can improve the health and quality of life of breast cancer survivors and increase the survival rate in patients with metastatic disease. In this respect, the field of cancer research has placed a particular emphasis on the elucidation of genetic and epigenetic alterations that may lead to the pathogenesis of breast cancer and contribute to its progression.     

Changes in tetrahydrobiopterin levels in endothelial cells and adult cardiomyocytes induced by LPS and hydrogen peroxide—A role for GFRP?

Alterations in tetrahydrobiopterin (BH4) levels have significant consequences in vascular pathophysiology. However, the mechanisms regulating BH4 remain poorly understood. The activity of GTP cyclohydrolase I (GTPCH-I), the first enzyme in BH4 biosynthesis, is controlled by protein levels, posttranslational modifications and interaction with GTPCH-I feedback regulatory protein (GFRP). This work examined the correlation between GTPCH-I protein levels and activity and changes in BH4 in human endothelial cells (HAECs) and adult rat cardiomyocytes (ARCM). Changes in BH4 were stimulated with LPS in HAECs and ARCM, and with hydrogen peroxide in HAECs only. Biopterin production by HAECs and ARCM were attained with concentrations of LPS >1 microg/ml and responses were nonlinear with respect to LPS concentrations. Western blot analysis demonstrated that induction of biopterin synthesis in HAECs and ARCM by LPS does not entail augmentation of constitutive GTPCH-I protein levels. However, LPS diminished GFRP mRNA, suggesting that disruption of GTPCH-I:GFRP complex enhances de novo biopterin synthesis. Conversely, treatment with hydrogen peroxide increased GTPCH-I and GFRP mRNA levels in HAECs while depleting BH4 and GSH, which was counteracted by catalase. This indicates that GFRP may override increases in GTPCH-I protein inhibiting enzyme activity. This conclusion is further supported by depletion of biopterin in cells transiently transfected with GFRP. Thus, allosteric regulation of GTPCH-I activity in the cardiovascular system maybe an important mechanism regulating BH4 levels through GFRP signaling.     

Evaluating quantum yield and ultraviolet–visible reflectance in baby pumpkins: Implications for oviposition behavior of pumpkin fruit flies

Frugivorous insects utilize both olfactory and visual cues to locate their host plants. Although volatiles have been extensively studied for detecting infested fruits, the role of visual cues in oviposition site selection remains mostly unknown among frugivorous insects. To investigate physiological changes in a host plant, we measured the quantum yield and reflectance of three wavelengths of light (350, 450 and 520 nm) after puncturing the surfaces of commercially grown pumpkins using insect pins during two different seasons outdoors. Quantum yields did not show significant differences between undamaged and simulated oviposition sites. Two wavelengths within the visual spectrum were similar between the two treatments. However, photon counts at 350 nm, in the ultraviolet range, were 1.76 fold higher in simulated oviposition sites than in undamaged sites, which was consistently observed across three field seasons. Considering that frugivorous insects and other phytophagous insects recognize the 350 nm wavelength for host identification and oviposition, we conclude that the disparities in ultraviolet reflectance can serve as a baseline for assessing the actual oviposition response of fruit flies. This finding contributes to the role of visual cues in the oviposition behavior of frugivorous insects and the development of a nondestructive detection method for pumpkin fruit flies.     

Seals and fisheries: A case for predator control?

The impact of seals on fisheries has been a controversial matter. This article examines the degree to which a new Canadian Royal Commission Report has been able to judge between the opposing views of the problem. It also examines the implications of the Commission's results for the more general question of controlling predators for the benefit of prey species, or more accurately, the human harvesters of those species. Finally, it touches very briefly on the possible clash of views between the public at large and those who make their living from the sea.