Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure

This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC₅) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions.     

Role of senataxin in DNA damage and telomeric stability

Ataxia with oculomotor apraxia type 2 (AOA2) is an autosomal recessive neurodegenerative disorder characterized by cerebellar ataxia and oculomotor apraxia. The gene mutated in AOA2, SETX, encodes senataxin (SETX), a putative DNA/RNA helicase. The presence of the helicase domain led us to investigate whether SETX might play a role in DNA damage repair and telomere stability. We analyzed the response of AOA2 lymphocytes and lymphoblasts after treatment with camptothecin (CPT), mitomycin C (MMC), H?O? and X-rays by cytogenetic and Q-FISH (quantitative-FISH) assays. The rate of chromosomal aberrations was normal in AOA2 cells after treatment with CPT, MMC, H?O? and X-rays. Conversely, Q-FISH analysis showed constitutively reduced telomere length in AOA2 lymphocytes, compared to age-matched controls. Furthermore, CPT- or X-ray-induced telomere shortening was more marked in AOA2 than in control cells. The partial co-localization of SETX with telomeric DNA, demonstrated by combined immunofluorescence-Q-FISH and chromatin immunoprecipitation, suggests a possible involvement of SETX in telomere stability.     

Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli.Indeed,diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits.Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels.In this review,we summarize the current knowledge of the interplay between phytoho...     

Processivity clamp gp45 and ssDNA-binding-protein gp32 modulate the fidelity of bacteriophage RB69 DNA polymerase in a sequence-specific manner, sometimes enhancing and sometimes compromising accuracy

Numerous studies of the impact of accessory proteins upon the fidelity of DNA synthesis have provided a complex and sometimes discordant picture. We previously described such an analysis conducted in vitro using various bacteriophage RB69 gp43 mutator DNA polymerases with or without the accessory proteins gp32 (which binds single-stranded DNA) plus gp45/44/62 (processivity clamp and its loaders). Mutations were scored at many sites in the lacZalpha mutation reporter sequence. Unexpectedly, the accessory proteins sometimes decreased and sometimes increased fidelity at a handful of specific sites. Here, we enlarge our analysis with one particular mutator polymerase compromised in both insertion accuracy and proofreading and also extend the analysis to reactions supplemented only with gp32 or only with gp45/44/62. An overall 1.56-fold increase in mutation frequencies was produced by adding single or multiple accessory proteins and was driven mainly by increased T(template)*G(primer) mispairs. Evidence was found for many additional sites where the accessory proteins influence fidelity, indicating the generality of the effect. Thus, accessory proteins contribute to the site-specific variability in mutation rates characteristically seen in mutational spectra.     

Epigenetic developmental mechanisms in plants: molecules and targets of plant epigenetic regulation

Genetic approaches to understanding the role of epigenetic regulation of gene expression in plants and its mechanisms have revealed several new components. Rapidly accumulating information from other eukaryotes provides complementary knowledge with important implications for plant research. Comparison of epigenetic events across species is proving critical for defining the mechanisms and functions of epigenetic modification, including those specific to plants.     

Genetic and epigenetic regulation of stress responses in natural plant populations

Plants have developed intricate mechanisms involving gene regulatory systems to adjust to stresses. Phenotypic variation in plants under stress is classically attributed to DNA sequence variants. More recently, it was found that epigenetic modifications - DNA methylation-, chromatin- and small RNA-based mechanisms - can contribute separately or together to phenotypes by regulating gene expression in response to the stress effect. These epigenetic modifications constitute an additional layer of complexity to heritable phenotypic variation and the evolutionary potential of natural plant populations because they can affect fitness. Natural populations can show differences in performance when they are exposed to changes in environmental conditions, partly because of their genetic variation but also because of their epigenetic variation. The line between these two components is blurred because little is known about the contribution of genotypes and epigenotypes to stress tolerance in natural populations. Recent insights in this field have just begun to shed light on the behavior of genetic and epigenetic variation in natural plant populations under biotic and abiotic stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.     

Activation and epigenetic regulation of DNA transposon nDart1 in rice

A large part of the rice genome is composed of transposons. Since active excision/reintegration of these mobile elements may result in harmful genetic changes, many transposons are maintained in a genetically or epigenetically inactivated state. However, some non-autonomous DNA transposons of the nDart1-3 subgroup, including nDart1-0, actively transpose in specific rice lines, such as pyl-v which carries an active autonomous element, aDart1-27, on chromosome 6. Although nDart1-3 subgroup elements show considerable sequence identity, they display different excision frequencies. The most active element, nDart1-0, had a low cytosine methylation status. The aDart1-27 sequence showed conservation between pyl-stb (pyl-v derivative line) and Nipponbare, which both lack autonomous activity for transposition of nDart1-3 subgroup elements. In pyl-v plants, the promoter region of the aDart1-27 transposase gene was more hypomethylated than in other rice lines. Treatment with the methylation inhibitor 5-azacytidine (5-azaC) induced transposition of nDart1-3 subgroup elements in both pyl-stb and Nipponbare plants; the new insertion sites were frequently located in genic regions. 5-AzaC treatment principally induced expression of Dart1-34 transposase rather than the other 38 aDart1-related elements in both pyl-stb and Nipponbare treatment groups. Our observations show that transposition of nDart1-3 subgroup elements in the nDart1/aDart1 tagging system is correlated with the level of DNA methylation. Our system does not cause somaclonal variation due to an absence of transformed plants, offers the possibility of large-scale screening in the field and can identify dominant mutants. We therefore propose that this tagging system provides a valuable addition to the tools available for rice functional genomics.     

Genetic and epigenetic stability of stem cells: Epigenetic modifiers modulate the fate of mesenchymal stem cells

Stem cell research has progressed widely and has been receiving a considerable attention for its advantages and drawbacks. Despite their extensive therapeutic potential in regenerative medicine, they are debatable for their genetic and epigenetic stability. In fact lineage specific differentiation is mediated via epigenetic changes in DNA methylation, acetylation, histone modifications etc. Thus epigenetics plays an important role in stem cell biology. For therapeutic interventions stem cells need to be genetically and epigenetically stable for their maximum paracrine secretions for bringing about expected tissue repair and regeneration. In this review we have focused on the current status of genetic and epigenetic stability in stem cells and their importance in regenerative medicine. We have also touched upon the possibility of considering tissue resident mesenchymal stem cells as epigenetic modifiers. This is likely to open a new era in stem cell therapeutic intervention by reversing disease inducing epigenetic changes.     

Climate change drives a shift in peatland ecosystem plant community: Implications for ecosystem function and stability

The composition of a peatland plant community has considerable effect on a range of ecosystem functions. Peatland plant community structure is predicted to change under future climate change, making the quantification of the direction and magnitude of this change a research priority. We subjected intact, replicated vegetated poor fen peat monoliths to elevated temperatures, increased atmospheric carbon dioxide (CO₂), and two water table levels in a factorial design to determine the individual and synergistic effects of climate change factors on the poor fen plant community composition. We identify three indicators of a regime shift occurring in our experimental poor fen system under climate change: nonlinear decline of Sphagnum at temperatures 8 °C above ambient conditions, concomitant increases in Carex spp. at temperatures 4 °C above ambient conditions suggesting a weakening of Sphagnum feedbacks on peat accumulation, and increased variance of the plant community composition and pore water pH through time. A temperature increase of +4 °C appeared to be a threshold for increased vascular plant abundance; however the magnitude of change was species dependent. Elevated temperature combined with elevated CO₂ had a synergistic effect on large graminoid species abundance, with a 15 times increase as compared to control conditions. Community analyses suggested that the balance between dominant plant species was tipped from Sphagnum to a graminoid‐dominated system by the combination of climate change factors. Our findings indicate that changes in peatland plant community composition are likely under future climate change conditions, with a demonstrated shift toward a dominance of graminoid species in poor fens.     

Different regulation of the p53 core domain activities 3'-to-5' exonuclease and sequence-specific DNA binding

In this study we further characterized the 3'-5' exonuclease activity intrinsic to wild-type p53. We showed that this activity, like sequence-specific DNA binding, is mediated by the p53 core domain. Truncation of the C-terminal 30 amino acids of the p53 molecule enhanced the p53 exonuclease activity by at least 10-fold, indicating that this activity, like sequence-specific DNA binding, is negatively regulated by the C-terminal basic regulatory domain of p53. However, treatments which activated sequence-specific DNA binding of p53, like binding of the monoclonal antibody PAb421, which recognizes a C-terminal epitope on p53, or a higher phosphorylation status, strongly inhibited the p53 exonuclease activity. This suggests that at least on full-length p53, sequence-specific DNA binding and exonuclease activities are subject to different and seemingly opposing regulatory mechanisms. Following up the recent discovery in our laboratory that p53 recognizes and binds with high affinity to three-stranded DNA substrates mimicking early recombination intermediates (C. Dudenhoeffer, G. Rohaly, K. Will, W. Deppert, and L. Wiesmueller, Mol. Cell. Biol. 18:5332-5342), we asked whether such substrates might be degraded by the p53 exonuclease. Addition of Mg2+ ions to the binding assay indeed started the p53 exonuclease and promoted rapid degradation of the bound, but not of the unbound, substrate, indicating that specifically recognized targets can be subjected to exonucleolytic degradation by p53 under defined conditions.     

Glucocorticoid-induced loss of DNA methylation in non-neuronal cells and potential involvement of DNMT1 in epigenetic regulation of Fkbp5

Glucocorticoids may play a significant role in the etiology of neuropsychiatric illnesses. Abnormalities in plasma cortisol levels, glucocorticoid sensitivity, and HPA-axis function often accompany clinical symptoms of stress-related illnesses such as PTSD and depression. Of particular interest are genetic association studies that link single nucleotide polymorphisms of HPA-axis genes with illnesses only in the context of an early-life trauma exposure such as child abuse. These studies suggest that dysregulation of HPA-axis function can have lasting repercussions in shaping mood and anxiety, long after termination of the traumatic experience. As persistent glucocorticoid-induced loss of DNA methylation in FK506 binding protein 5 (Fkbp5) was previously observed in the hippocampus and blood and in the neuronal cell line HT-22, we asked whether these epigenetic alterations occur in non-neuronal, HPA-axis relevant cells. We used the pituitary adenoma cell line AtT-20 to demonstrate that the intronic enhancer region of Fkbp5 undergoes loss of DNA methylation in response to dexamethasone treatment in a dose-dependent manner. We also focused on the mouse hippocampal dentate gyrus to test whether these changes would be enriched in a region implicated in the HPA-axis stress response, neurogenesis, and synaptic plasticity. We observed an increase in enrichment of DNA methylation loss in the dentate gyrus, as compared to whole hippocampal tissues that were similarly treated with glucocorticoids. We then asked whether DNA methyltransferase 1 (Dnmt1), a methyltransferase enzyme involved in maintaining DNA methylation following cell division, is involved in the observed epigenetic alterations. We found a dose-dependent decrease of Dnmt1 expression in the AtT-20 cells following dexamethasone treatment, and a similar decrease in corticosterone-treated mouse hippocampus. Taken together, we provide evidence that these glucocorticoid-induced epigenetic alterations have a broader validity in non-neuronal cells and that they may involve the DNA methylation machinery.     

Application of novel nanotechnology strategies in plant biotransformation: a contemporary overview

During the past epoch we have gone through the remarkable progress in plant gene transformation technology. The production of transgenic plants is considered as a valuable tool in plant research and the technology is extensively applied in phytomedicines and agricultural research. Gene transformation in plants is normally carried out by Agrobacterium species, application of some chemicals and physical techniques (electroporation, microprojectile, etc.). Now a days with better efficacy and reproducibility, novel technologies for the direct gene transfer like liposome, positively charged liposome (lipofectin) and nanoparticle based delivery systems are used for genetic transformation of plants. In this review, we have enlightened the novel nanotechnologies like liposome, Carbon nano-tube and nanoparticles with their current status and future prospects in transgenic plant development. Moreover, we have also highlighted the limitations of conventional techniques of gene transfer. Furthermore, we have tried to postulate innovative ideas on the footprints of established nanotechnology and chemical based strategy with improved efficacy, reproducibility and accuracy along with less time consumption.