Genome flux in tomato auto- and auxo-trophic cell clones cultured in different auxin/cytokinin equilibria. I. DNA multiplicity and methylation levels

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 902-912 ◽  
Author(s):  
Patrizia Bogani ◽  
Alessandra Simoni ◽  
Priscilla Bettini ◽  
Maria Mugnai ◽  
M. Gabriella Pellegrini ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Significant Variation ◽  
Physiological State ◽  
Leaf Tissue ◽  
Dna Amplification ◽  
Epigenetic Changes ◽  
Physiological Conditions ◽  
Cell Clones ◽  
Methylation Patterns ◽  
Hormonal Treatments

An analysis of the effect of changing physiological conditions on genetic stability, in terms of epigenetic changes, such as DNA, methylation patterns, and multiplicity of repetitive DNA, was carried out on tomato cell clones grown on media supplemented with different auxin/cytokinin ratios. The effect of endogenous variation in phytohormone equilibria was also indirectly analysed through a comparison of auxotrophic or habituated (autotrophic) cell clones and the differentiated leaf tissue. The data obtained showed significant variation in methylation and multiplicity levels both between clones and between treatments, clearly suggesting a contemporary influence of exogenous hormonal treatments and of the initial/endogenous physiological state of the treated tissue on both phenomena studied.Key words: tomato clones, somaclonal variation, methylation, DNA amplification.

scholarly journals Parenting stress and DNA methylation among African Americans in the InterGEN Study

2017 ◽  
Vol 1 (6) ◽  
pp. 328-333 ◽  
Author(s):  
Michelle L. Wright ◽  
Yunfeng Huang ◽  
Qin Hui ◽  
Kevin Newhall ◽  
Cindy Crusto ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Parenting Stress ◽  
Mixed Models ◽  
Life Stress ◽  
Significant Variation ◽  
African Ancestry ◽  
Maternal Parenting ◽  
Maternal Parenting Stress ◽  
Methylation Patterns ◽  
The Relationship

IntroductionGeneral life stress has been associated with altered DNA methylation in individuals of African Ancestry, although the relationship between parenting stress and DNA methylation has not been described. The purpose of this study was to examine the relationship between maternal parenting stress and DNA methylation among African Ancestry mother-child dyads.MethodsWe evaluated epigenome-wide DNA methylation relative to parenting stress in 74 mother-child dyads using linear mixed models.ResultsSignificant variation in maternal DNA methylation at 95 CpG sites was associated with level of parenting stress. Notably, we identified a change in DNA methylation associated with poly (ADP-ribose) polymerase-1, which plays a key role in stress signaling. We did not identify any significant variation in child DNA methylation related to maternal parenting stress.ConclusionsHowever, DNA methylation patterns observed in children mirrored patterns observed in their mothers. The results suggest that differential maternal DNA methylation is associated with higher levels of parenting stress.

scholarly journals Insertion of Foreign DNA into an Established Mammalian Genome Can Alter the Methylation of Cellular DNA Sequences

1999 ◽  
Vol 73 (2) ◽  
pp. 1010-1022 ◽  
Author(s):  
Ralph Remus ◽  
Christina Kämmer ◽  
Hilde Heller ◽  
Birgit Schmitz ◽  
Gudrun Schell ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Lines ◽  
Mammalian Genome ◽  
Dna Integration ◽  
Bhk21 Cell ◽  
Cellular Genes ◽  
Cell Clones ◽  
Dna Insertion ◽  
Foreign Dna ◽  
Methylation Patterns

ABSTRACT The insertion of adenovirus type 12 (Ad12) DNA into the hamster genome and the transformation of these cells by Ad12 can lead to marked alterations in the levels of DNA methylation in several cellular genes and DNA segments. Since such alterations in DNA methylation patterns are likely to affect the transcription patterns of cellular genes, it is conceivable that these changes have played a role in the generation or the maintenance of the Ad12-transformed phenotype. We have now isolated clonal BHK21 hamster cell lines that carry in their genomes bacteriophage λ and plasmid pSV2neo DNAs in an integrated state. Most of these cell lines contain one or multiple copies of integrated λ DNA, which often colocalize with the pSV2neo DNA, usually in a single chromosomal site as determined by the fluorescent in situ hybridization technique. In different cell lines, the loci of foreign DNA insertion are different. The inserted bacteriophage λ DNA frequently becomes de novo methylated. In some of the thus-generated hamster cell lines, the levels of DNA methylation in the retrotransposon genomes of the endogenous intracisternal A particles (IAP) are increased in comparison to those in the non-λ-DNA-transgenic BHK21 cell lines. These changes in the methylation patterns of the IAP subclone I (IAPI) segment have been documented by restriction analyses with methylation-sensitive restriction endonucleases followed by Southern transfer hybridization and phosphorimager quantitation. The results of genomic sequencing experiments using the bisulfite protocol yielded additional evidence for alterations in the patterns of DNA methylation in selected segments of the IAPI sequences. In these experiments, the nucleotide sequences in >330 PCR-generated cloned DNA molecules were determined. Upon prolonged cultivation of cell lines with altered cellular methylation patterns, these differences became less apparent, perhaps due to counterselection of the transgenic cells. The possibility existed that the hamster BHK21 cell genomes represent mosaics with respect to DNA methylation in the IAPI segment. Hence, some of the cells with the patterns observed after λ DNA integration might have existed prior to λ DNA integration and been selected by chance. A total of 66 individual BHK21 cell clones from the BHK21 cell stock have been recloned up to three times, and the DNAs of these cell populations have been analyzed for differences in IAPI methylation patterns. None have been found. These patterns are identical among the individual BHK21 cell clones and identical to the patterns of the originally used BHK21 cell line. Similar results have been obtained with nine clones isolated from BHK21 cells mock transfected by the Ca2+-phosphate precipitation procedure with DNA omitted from the transfection mixture. In four clonal sublines of nontransgenic control BHK21 cells, genomic sequencing of 335 PCR-generated clones by the bisulfite protocol revealed 5′-CG-3′ methylation levels in the IAPI segment that were comparable to those in the uncloned BHK21 cell line. We conclude that the observed changes in the DNA methylation patterns in BHK21 cells with integrated λ DNA are unlikely to preexist or to be caused by the transfection procedure. Our data support the interpretation that the insertion of foreign DNA into a preexisting mammalian genome can alter the cellular patterns of DNA methylation, perhaps via changes in chromatin structure. The cellular sites affected by and the extent of these changes could depend on the site and size of foreign DNA insertion.

scholarly journals Detection of LINE-1 hypomethylation in cfDNA of Esophageal Adenocarcinoma Patients

2020 ◽  
Vol 21 (4) ◽  
pp. 1547 ◽  
Author(s):  
Elisa Boldrin ◽  
Matteo Curtarello ◽  
Marco Dallan ◽  
Rita Alfieri ◽  
Stefano Realdon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Esophageal Adenocarcinoma ◽  
Methodological Approach ◽  
Methylation Status ◽  
Dna Amplification ◽  
Restriction Enzymes ◽  
Poor Quality ◽  
Bisulfite Conversion ◽  
Dna Hypomethylation ◽  
Methylation Patterns

DNA methylation plays an important role in cancer development. Cancer cells exhibit two types of DNA methylation alteration: site-specific hypermethylation at promoter of oncosuppressor genes and global DNA hypomethylation. This study evaluated the methylation patterns of long interspersed nuclear element (LINE-1) sequences which, due to their relative abundance in the genome, are considered a good surrogate indicator of global DNA methylation. LINE-1 methylation status was investigated in the cell-free DNA (cfDNA) of 21 patients, 19 with esophageal adenocarcinoma (EADC) and 2 with Barrett’s esophagus (BE). The two BE patients and one EADC patient were also analyzed longitudinally. Methylation status was analyzed using restriction enzymes and DNA amplification. This methodology was chosen to avoid bisulfite conversion, which we considered inadequate for cfDNA analysis. Indeed, cfDNA is characterized by poor quality and low concentration, and bisulfite conversion might worsen these conditions. Results showed that hypomethylated LINE-1 sequences are present in EADC cfDNA. Furthermore, longitudinal studies in BE suggested a correlation between methylation status of LINE-1 sequences in cfDNA and progression to EADC. In conclusion, our study indicated the feasibility of our methodological approach to detect hypomethylation events in cfDNA from EADC patients, and suggests LINE-1 methylation analysis as a new possible molecular assay to integrate into patient monitoring.

scholarly journals Epigenetic aging of human hematopoietic cells is not accelerated upon transplantation into mice

2018 ◽  
Author(s):  
Joana Frobel ◽  
Susann Rahmig ◽  
Julia Franzen ◽  
Claudia Waskow ◽  
Wolfgang Wagner
Keyword(s):  
Dna Methylation ◽  
Epigenetic Clock ◽  
Epigenetic Changes ◽  
Hematopoietic Stem ◽  
Hematopoietic Development ◽  
Immunodeficient Mice ◽  
Epigenetic Aging ◽  
Normal Human ◽  
Methylation Patterns

AbstractTransplantation of human hematopoietic stem cells into immunodeficient mice provides a powerful in vivo model system to gain functional insights into hematopoietic differentiation. So far, it remains unclear if epigenetic changes of normal human hematopoiesis are recapitulated upon engraftment into such “humanized mice”. Mice have a much shorter life expectancy than men, and therefore we hypothesized that the xenogeneic environment might greatly accelerate the epigenetic clock. We demonstrate that genome-wide DNA methylation patterns of normal human hematopoietic development are indeed recapitulated upon engraftment in mice – particularly those of normal early B cell progenitor cells. Furthermore, we tested three epigenetic aging signatures and none of them indicated that the murine environment accelerated age-associated DNA methylation changes. These results demonstrate that the murine transplantation model overall recapitulates epigenetic changes of human hematopoietic development, whereas epigenetic aging seems to occur cell intrinsically.

DNA Methylation in Placentas of Interspecies Mouse Hybrids

Genetics ◽  
2003 ◽  
Vol 165 (1) ◽  
pp. 223-228
Author(s):  
Sabine Schütt ◽  
Andrea R Florl ◽  
Wei Shi ◽  
Myriam Hemberger ◽  
Annie Orth ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Basis ◽  
Interspecific Hybrids ◽  
Genetic System ◽  
Differential Methylation ◽  
Late Gestation ◽  
Epigenetic Changes ◽  
Repeat Sequences ◽  
Mouse Placenta ◽  
Methylation Patterns

Abstract Interspecific hybridization in the genus Mus results in several hybrid dysgenesis effects, such as male sterility and X-linked placental dysplasia (IHPD). The genetic or molecular basis for the placental phenotypes is at present not clear. However, an extremely complex genetic system that has been hypothesized to be caused by major epigenetic changes on the X chromosome has been shown to be active. We have investigated DNA methylation of several single genes, Atrx, Esx1, Mecp2, Pem, Psx1, Vbp1, Pou3f4, and Cdx2, and, in addition, of LINE-1 and IAP repeat sequences, in placentas and tissues of fetal day 18 mouse interspecific hybrids. Our results show some tendency toward hypomethylation in the late gestation mouse placenta. However, no differential methylation was observed in hyper- and hypoplastic hybrid placentas when compared with normal-sized littermate placentas or intraspecific Mus musculus placentas of the same developmental stage. Thus, our results strongly suggest that generalized changes in methylation patterns do not occur in trophoblast cells of such hybrids.

scholarly journals Integrated Analysis of DNA Methylome and Transcriptome Reveals Epigenetic Regulation of CAM Photosynthesis in Pineapple

2020 ◽  
Author(s):  
Haifeng Wang ◽  
Yan Shi ◽  
Xingtan Zhang ◽  
Xiaojun Chang ◽  
Maokai Yan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Time Course ◽  
Carbon Fixation ◽  
Leaf Tissue ◽  
Integrated Analysis ◽  
Arid Environments ◽  
Dna Methylome ◽  
Use Efficiency ◽  
Methylation Patterns ◽  
Cam Photosynthesis

Abstract Background: Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood. Results: Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH. Conclusions: Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.

scholarly journals Global DNA Methylation Patterns in Human Gliomas and Their Interplay with Other Epigenetic Modifications

2019 ◽  
Vol 20 (14) ◽  
pp. 3478 ◽  
Author(s):  
Michal J. Dabrowski ◽  
Bartosz Wojtas
Keyword(s):  
Dna Methylation ◽  
Histone Modifications ◽  
Global Gene Expression ◽  
Global Dna Methylation ◽  
Epigenetic Changes ◽  
Human Gliomas ◽  
Human Pathology ◽  
Different Types ◽  
Methylation Patterns ◽  
The Impact

During the last two decades, several international consortia have been established to unveil the molecular background of human cancers including gliomas. As a result, a huge outbreak of new genetic and epigenetic data appeared. It was not only shown that gliomas share some specific DNA sequence aberrations, but they also present common alterations of chromatin. Many researchers have reported specific epigenetic features, such as DNA methylation and histone modifications being involved in tumor pathobiology. Unlike mutations in DNA, epigenetic changes are more global in nature. Moreover, many studies have shown an interplay between different types of epigenetic changes. Alterations in DNA methylation in gliomas are one of the best described epigenetic changes underlying human pathology. In the following work, we present the state of knowledge about global DNA methylation patterns in gliomas and their interplay with histone modifications that may affect transcription factor binding, global gene expression and chromatin conformation. Apart from summarizing the impact of global DNA methylation on glioma pathobiology, we provide an extract of key mechanisms of DNA methylation machinery.

scholarly journals DNA Methylation of TLR4, VEGFA, and DEFA5 Is Associated With Necrotizing Enterocolitis in Preterm Infants

2021 ◽  
Vol 9 ◽  
Author(s):  
Daphne H. Klerk ◽  
Torsten Plösch ◽  
Rikst Nynke Verkaik-Schakel ◽  
Jan B. F. Hulscher ◽  
Elisabeth M. W. Kooi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Preterm Infants ◽  
Necrotizing Enterocolitis ◽  
Epigenetic Changes ◽  
Non Invasive ◽  
Invasive Method ◽  
Observational Cohort ◽  
Stool Samples ◽  
Methylation Patterns ◽  
Short Time

Background: Epigenetic changes, such as DNA methylation, may contribute to an increased susceptibility for developing necrotizing enterocolitis (NEC) in preterm infants. We assessed DNA methylation in five NEC-associated genes, selected from literature: EPO, VEGFA, ENOS, DEFA5, and TLR4 in infants with NEC and controls.Methods: Observational cohort study including 24 preterm infants who developed NEC (≥Bell Stage IIA) and 45 matched controls. DNA was isolated from stool samples and methylation measured using pyrosequencing. We investigated differences in methylation prior to NEC compared with controls. Next, in NEC infants, we investigated methylation patterns long before, a short time before NEC onset, and after NEC.Results: Prior to NEC, only TLR4 CpG 2 methylation was increased in NEC infants (median = 75.4%, IQR = 71.3–83.8%) versus controls (median = 69.0%, IQR = 64.5–77.4%, p = 0.025). In NEC infants, VEGFA CpG 3 methylation was 0.8% long before NEC, increasing to 1.8% a short time before NEC and 2.0% after NEC (p = 0.011; p = 0.021, respectively). A similar pattern was found in DEFA5 CpG 1, which increased from 75.4 to 81.4% and remained 85.3% (p = 0.027; p = 0.019, respectively). These changes were not present for EPO, ENOS, and TLR4.Conclusion: Epigenetic changes of TLR4, VEGFA, and DEFA5 are present in NEC infants and can differ in relation to the time of NEC onset. Differences in DNA methylation of TLR4, VEGFA, and DEFA5 may influence gene expression and increase the risk for developing NEC. This study also demonstrates the use of human DNA extraction from stool samples as a novel non-invasive method for exploring the bowel of preterm infants and which can also be used for necrotizing enterocolitis patients.

scholarly journals Altered DNA Methylation Patterns Associated With Clinically Relevant Increases in PTSD Symptoms and PTSD Symptom Profiles in Military Personnel

2018 ◽  
Vol 20 (3) ◽  
pp. 352-358 ◽  
Author(s):  
Christiana Martin ◽  
Young-Eun Cho ◽  
Hyungsuk Kim ◽  
Sijung Yun ◽  
Rebekah Kanefsky ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Military Personnel ◽  
Axonal Guidance ◽  
Epigenetic Changes ◽  
Ptsd Symptoms ◽  
Cross Sectional ◽  
Canonical Pathways ◽  
Longitudinal Comparison ◽  
Clinical Changes ◽  
Methylation Patterns

Military personnel experience posttraumatic stress disorder (PTSD), which is associated with differential DNA methylation across the whole genome. However, the relationship between these DNA methylation patterns and clinically relevant increases in PTSD severity is not yet clearly understood. The purpose of this study was to identify differences in DNA methylation associated with PTSD symptoms and investigate DNA methylation changes related to increases in the severity of PTSD in military personnel. In this pilot study, a cross-sectional comparison was made between military personnel with PTSD (n = 8) and combat-matched controls without PTSD (n = 6). Symptom measures were obtained, and genome-wide DNA methylation was measured using methylated DNA immunoprecipitation (MeDIP-seq) from whole blood samples at baseline and 3 months later. A longitudinal comparison measured DNA methylation changes in military personnel with clinically relevant increases in PTSD symptoms between time points (PTSD onset) and compared methylation patterns to controls with no clinical changes in PTSD. In military personnel with elevated PTSD symptoms 3 months following baseline, 119 genes exhibited reduced methylation and 8 genes exhibited increased methylation. Genes with reduced methylation in the PTSD-onset group relate to the canonical pathways of netrin signaling, Wnt/Ca+ pathway, and axonal guidance signaling. These gene pathways relate to neurological disorders, and the current findings suggest that these epigenetic changes potentially relate to PTSD symptomology. This study provides some novel insights into the role of epigenetic changes in PTSD symptoms and the progression of PTSD symptoms in military personnel.

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