Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid

Genome ◽  
2011 ◽  
Vol 54 (1) ◽  
pp. 42-49 ◽  
Author(s):  
Beery Yaakov ◽  
Khalil Kashkush
Keyword(s):  
Cytosine Methylation ◽  
Genomic Rearrangements ◽  
Site Specific ◽  
Transposon Display ◽  
Genomic Changes ◽  
Specific Pcr ◽  
Two Generations ◽  
Insertion Sites ◽  
High Level ◽  
Methylation Patterns

Rapid and reproducible genomic changes can be induced during the early stages of the life of nascent allopolyploid species. In a previous study, it was shown that following allopolyploidization, cytosine methylation changes can affect up to 11% of the wheat genome. However, the methylation patterns around transposable elements (TEs) were never studied in detail. We used transposon methylation display (TMD) to assess the methylation patterns of CCGG sites flanking three TE families (Balduin, Apollo, and Thalos) in the first four generations of a newly formed wheat allohexaploid. In addition, transposon display (TD), using a methylation-insensitive restriction enzyme, was applied to search for genomic rearrangements at the TE insertion sites. We observed that up to 54% of CCGG sites flanking the three TE families showed changes in methylation patterns in the first four generations of a newly formed wheat allohexaploid, where hypermethylation was predominant. Over 70% of the changes in TMD patterns occurred in the first two generations of the newly formed allohexaploid. Furthermore, analysis of 555 TE insertion sites by TD and 18 cases by site-specific PCR revealed a full additive pattern in the allohexaploid, an indication for lack of massive rearrangements. These data indicate that following allopolyplodization, DNA-TE insertion sites can undergo a significantly high level of methylation changes compared with methylation changes of other genomic sequences.

scholarly journals Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome

2017 ◽  
Vol 4 (9) ◽  
pp. 170248 ◽  
Author(s):  
Laura Welsh ◽  
Ryszard Maleszka ◽  
Sylvain Foret
Keyword(s):  
Cytosine Methylation ◽  
Amplicon Sequencing ◽  
Cell Types ◽  
Cellular Processes ◽  
Novel Approach ◽  
Asymmetric Methylation ◽  
High Level ◽  
Methylation Patterns ◽  
Cg Dinucleotides ◽  
Honeybee Genome

Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here, we have applied a novel approach to examine whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, a social insect with a high level of epigenetically driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics, we show that rare asymmetrically methylated CpGs can be unambiguously detected in the honeybee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric.

Site-specific methylation patterns of theGALandGALR1/2genes in head and neck cancer: Potential utility as biomarkers for prognosis

2016 ◽  
Vol 56 (3) ◽  
pp. 1107-1116 ◽  
Author(s):  
Kiyoshi Misawa ◽  
Daiki Mochizuki ◽  
Shiori Endo ◽  
Masato Mima ◽  
Yuki Misawa ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Head And Neck ◽  
Neck Cancer ◽  
Potential Utility ◽  
Site Specific ◽  
Methylation Patterns

scholarly journals Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B

2020 ◽  
Vol 48 (7) ◽  
pp. 3949-3961 ◽  
Author(s):  
Chien-Chu Lin ◽  
Yi-Ping Chen ◽  
Wei-Zen Yang ◽  
James C K Shen ◽  
Hanna S Yuan
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Cytosine Methylation ◽  
Catalytic Domain ◽  
De Novo ◽  
Water Channel ◽  
Dna Methyltransferases ◽  
Structural Basis ◽  
Cpg Sites ◽  
Methylation Patterns

Abstract DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B–3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.

scholarly journals Molecular characterization and phylogenetic analysis of one Omega-gliadin gene from Aegilops speltoidesl

Genetika ◽  
2018 ◽  
Vol 50 (2) ◽  
pp. 503-517 ◽  
Author(s):  
Wanqing Wang ◽  
Ke Wang ◽  
Xi Chen ◽  
Slaven Prodanovic ◽  
Xiaohui Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Quality Improvement ◽  
Related Species ◽  
Storage Proteins ◽  
Aegilops Speltoides ◽  
Amino Acid Residues ◽  
Sequence Characterization ◽  
Specific Pcr ◽  
High Level ◽  
Wheat Storage Proteins

Gliadins, as the major components of wheat storage proteins, determine the extensibility properties of dough and have important effects on flour processing quality. Wheat related species carries potential storage protein gene resources for quality improvement. In this study, we isolated and characterized the first complete ?-gliadin gene Omega-AS from Aegilops speltoides L. (2n = 2x = 14, SS) by allelic-specific PCR and investigated its phylogenetic relationships among Triticum and Aegilopsspecies. Molecular structure showed that Omega-AS gene consisted of 1122 bp encoding 373 amino acid residues with deduced molecular mass 41379.21 Da. Omega-AS gene was exceptionally rich in prolines and glutamines with fewer methionine and no cysteine. Sequence characterization and epitope analysis showed that three epitopes QQPIPVQPQQ, TQPQQPTPIQ and IQPQQPFPQQ were absent in Omega-AS gene encoded protein, indicating its potential value for wheat quality improvement with less toxic, or no toxic peptides. Phylogenetic analysis revealed that Omega-AS was closely related to gliadin genes of wheat and related species and its divergence from bread wheat was more recently (less than 1.243 MYA). Heterologous expression showed that Omega-AS gene could successfully express with a high level in E. coli under the control of T7promoter. The transcription expression pattern of Omega-AS gene during grain development detected by qRT-PCR revealed that the highest expression level occurred at 17 days post an thesis.

scholarly journals Stochastic Modeling Reveals Kinetic Heterogeneity in Post-replication DNA Methylation

2019 ◽  
Author(s):  
Luis Busto-Moner ◽  
Julien Morival ◽  
Arjang Fahim ◽  
Zachary Reitz ◽  
Timothy L. Downing ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Dna Methylation ◽  
Rate Constants ◽  
Cytosine Methylation ◽  
Temporal Dynamics ◽  
Epigenetic Modification ◽  
Embryonic Stem ◽  
Likelihood Estimation ◽  
Dna Methyltransferases ◽  
Methylation Patterns

AbstractDNA methylation is a heritable epigenetic modification that plays an essential role in mammalian development. Genomic methylation patterns are dynamically maintained, with DNA methyltransferases mediating inheritance of methyl marks onto nascent DNA over cycles of replication. A recently developed experimental technique employing immunoprecipitation of bromodeoxyuridine labeled nascent DNA followed by bisulfite sequencing (Repli-BS) measures post-replication temporal evolution of cytosine methylation, thus enabling genome-wide monitoring of methylation maintenance. In this work, we combine statistical analysis and stochastic mathematical modeling to analyze Repli-BS data from human embryonic stem cells. We estimate site-specific kinetic rate constants for the restoration of methyl marks on >10 million uniquely mapped cytosines within the CpG (cytosine-phosphate-guanine) dinucleotide context across the genome using Maximum Likelihood Estimation. We find that post-replication remethylation rate constants span approximately two orders of magnitude, with half-lives of per-site recovery of steady-state methylation levels ranging from shorter than ten minutes to five hours and longer. Furthermore, we find that kinetic constants of maintenance methylation are correlated among neighboring CpG sites. Stochastic mathematical modeling provides insight to the biological mechanisms underlying the inference results, suggesting that enzyme processivity and/or collaboration can produce the observed kinetic correlations. Our combined statistical/mathematical modeling approach expands the utility of genomic datasets and disentangles heterogeneity in methylation patterns arising from replication-associated temporal dynamics versus stable cell-to-cell differences.

scholarly journals Epigenetic changes in fibroblasts drive cancer metabolism and differentiation

2019 ◽  
Vol 26 (12) ◽  
pp. R673-R688 ◽  
Author(s):  
Rajeev Mishra ◽  
Subhash Haldar ◽  
Surabhi Suchanti ◽  
Neil A Bhowmick
Keyword(s):  
Prostate Cancer ◽  
Cancer Progression ◽  
Cancer Metabolism ◽  
Promoter Hypermethylation ◽  
Ras Signaling ◽  
Androgen Receptor Signaling ◽  
Genomic Changes ◽  
Signaling Axis ◽  
Carcinoma Associated Fibroblasts ◽  
Methylation Patterns

Genomic changes that drive cancer initiation and progression contribute to the co-evolution of the adjacent stroma. The nature of the stromal reprogramming involves differential DNA methylation patterns and levels that change in response to the tumor and systemic therapeutic intervention. Epigenetic reprogramming in carcinoma-associated fibroblasts are robust biomarkers for cancer progression and have a transcriptional impact that support cancer epithelial progression in a paracrine manner. For prostate cancer, promoter hypermethylation and silencing of the RasGAP, RASAL3 that resulted in the activation of Ras signaling in carcinoma-associated fibroblasts. Stromal Ras activity initiated a process of macropinocytosis that provided prostate cancer epithelia with abundant glutamine for metabolic conversion to fuel its proliferation and a signal to transdifferentiate into a neuroendocrine phenotype. This epigenetic oncogenic metabolic/signaling axis seemed to be further potentiated by androgen receptor signaling antagonists and contributed to therapeutic resistance. Intervention of stromal signaling may complement conventional therapies targeting the cancer cell.

scholarly journals Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii

2014 ◽  
Author(s):  
Jean-Christophe Avarre ◽  
Bruno Guinand ◽  
Rémi Dugué ◽  
Jacky Cosson ◽  
Marc Legendre ◽  
...  
Keyword(s):  
Gene Expression ◽  
Natural Habitat ◽  
Expression Patterns ◽  
Osmotic Tolerance ◽  
Two Generations ◽  
Hypersaline Water ◽  
Significant Expression ◽  
Physiological Impact ◽  
High Level ◽  
Sarotherodon Melanotheron

The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water, in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.

The chromian spinels of the Lyavaraka ultrabasic complex, Serpentinite Belt, Kola Peninsula, Russia: Patterns of zoning, hypermagnesian compositions, and early oxidation

2021 ◽  
Vol 59 (6) ◽  
pp. 1693-1709
Author(s):  
Andrei Y. Barkov ◽  
Andrey A. Nikiforov ◽  
Vladimir N. Korolyuk ◽  
Larisa P. Barkova ◽  
Robert F. Martin
Keyword(s):  
Kola Peninsula ◽  
First Generation ◽  
Ferric Iron ◽  
Chromian Spinel ◽  
Maximum Value ◽  
Two Generations ◽  
High Level ◽  
A Minor ◽  
Compositional Series ◽  
Minor Quantity

ABSTRACT The maximum value of Mg# [= 100Mg/(Mg + Fe2+ + Mn)] in chromium-bearing spinel-group minerals (Chr) in the Ultrabasic Core Zone (UCZ) of the Lyavaraka orthopyroxenite – harzburgite – dunite complex of the Serpentinite Belt in the Kola Peninsula is 54.5–67.5. Such highly magnesian compositions of spinel are associated with notable enrichments of ferric iron (Fe3+# 58–63). There are two generations of accessory Chr in the UCZ unit. The first generation occurs as inclusions in olivine that is not unusually magnesian (Mg# 90.3), and the second is closely associated with serpentine. The compositional series of Chr at Lyavaraka attains more aluminous compositions than was observed in nearby intrusive bodies. The anomalously high level of Mg in Chr, also manifest in ilmenite, is mainly a result of the high intrinsic fugacity of oxygen attained locally in the melt. A progressive buildup in H2O and increase in fO2 likely resulted from efficient vesiculation and selective loss of H2 from the Al-undepleted komatiitic magma crystallizing in a shallow setting. The chromian spinel forming in such a modified magma is virtually unzoned in Mn, and a minor quantity of Mn is also present in olivine and orthopyroxene. In contrast, zinc is strongly partitioned in the core of Chr, as it is relatively incompatible in the coexisting olivine and orthopyroxene at that stage. Zinc efficiently partitioned into the H2O-enriched melt, which crystallized as the pegmatitic orthopyroxenite near the contacts at Lyavaraka. A high potential of oxidation appears to be characteristic of all orthopyroxenite – harzburgite – dunite suites of the Serpentinite Belt formed from a primitive melt of komatiitic composition.

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