scholarly journals Assessment of genetic and epigenetic variations in potato somatic hybrids by Methylation-sensitive ISSR and RAPD markers

2015 ◽  
Vol 44 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Jagesh Kumar Tiwari ◽  
Shaumaya Saurabh ◽  
Poonam Chandel ◽  
Bir Pal Singh ◽  
Vinay Bhardwaj
Keyword(s):  
Dna Methylation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Somatic Hybrids ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Mother Plant ◽  
Epigenetic Changes ◽  
Mother Plants ◽  
Methylation Patterns

Genetic and epigenetic changes (DNA methylation) in the mother plants of somatic hybrids (1st cycle) and their regenerants (30th cycles sub-cultured) were analyzed using methylation-sensitive ISSR and RAPD markers. ISSR and RAPD profiles and their cluster analyses based on the Jaccard’s similarity coefficient revealed 100% genetic similarity among the mother plant and their regenerants. While for the epigenetic changes in the samples, the MS-ISSR markers detected DNA methylation (2.7%) in the regenerants compared to the mother plant (1%), whereas MS-RAPD markers detected a little methylation patterns in the regeneratns (0.6%) compared to the mother plants (0.4%). DOI: http://dx.doi.org/10.3329/bjb.v44i1.22722 Bangladesh J. Bot. 44(1): 45-50, 2015 (March)

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.

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 Molecular Characterization of Saffron-Potential Candidates for Crop Improvement

2015 ◽  
Vol 7 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Javid Iqbal MIR ◽  
Nazeer AHMED ◽  
Mudasir Hafiz KHAN ◽  
Taseem Ahmad MOKHDOMI ◽  
Sajad Hussian WANI ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Ssr Markers ◽  
Significant Variation ◽  
Rapd Markers ◽  
Crop Improvement ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Improvement Programs ◽  
Rapd And Issr

In this study, thirty one (31) morphologically distinct selections of saffron crop were used for molecular characterization. Molecular characterization was done through SSR, ISSR and RAPD markers. RAPD and ISSR markers showed significant variation; however, SSR markers did not reveal any variation between the selected clones. The Jaccard’s similarity coefficient ranged from 0.94 to 1.00 with an average of 0.98 among all 31 selections used. Minimum similarity value (0.94) was observed between CITH-S-107 and PAM-S-116 selections. The study provides sufficient knowledge to identify clones with better stigma characteristics for further crop improvement programs.

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 Genetic Diversity between Yacon Landraces from Different Countries Based on Random Amplified Polymorphic DNAs

2011 ◽  
Vol 41 (No. 2) ◽  
pp. 73-78 ◽  
Author(s):  
L. Milella ◽  
J. Salava ◽  
G. Martelli ◽  
I. Greco ◽  
E.F. Cusimamani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Genetic Similarity ◽  
Morphological Traits ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Crop Germplasm ◽  
Relationship Of

Random amplified polymorphic DNA (RAPD) markers are widely used for evaluating the genetic relationship of crop germplasm. Five different landraces of yacon (Smallantus sonchifolius (Poepp. and Hendl.) H. Robinson; Asteraceae) collected in various countries and showing different morphological traits were investigated using a total of 61 decamer primers. A total of 282 RAPD markers were scored and 28.7% of them were polymorphic at least within landraces. RAPD markers generated by one primer (OBP14) discriminated between all landraces. Markers were used to calculate genetic similarity coefficient and to build a dendrogram representing the genetic relationship between analysed landraces. The results suggest that RAPD markers could be used as a reliable tool to perform fingerprinting studies in Smallantus sonchifolius genome. This is the first report on the use of RAPDs to evaluate genetic distance and to distinguish between different landraces in yacon.  

scholarly journals Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 457
Author(s):  
HyokChol Kim ◽  
Pei Lei ◽  
Aizhi Wang ◽  
Shuo Liu ◽  
Yong Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Castor Bean ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Ricinus Communis ◽  
Similarity Coefficient ◽  
Morphological Data ◽  
Oilseed Crop ◽  
Ricinus Communis L ◽  
Polymorphic Bands

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

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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