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.

scholarly journals Investigation of measurable residual disease in acute myeloid leukemia by DNA methylation patterns

Leukemia ◽  
2021 ◽  
Author(s):  
Tanja Božić ◽  
Chao-Chung Kuo ◽  
Jan Hapala ◽  
Julia Franzen ◽  
Monika Eipel ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Residual Disease ◽  
Amplicon Sequencing ◽  
Multiparametric Flow Cytometry ◽  
Methylation Patterns ◽  
Cg Dinucleotides ◽  
Measurable Residual Disease ◽  
Acute Myeloid

AbstractAssessment of measurable residual disease (MRD) upon treatment of acute myeloid leukemia (AML) remains challenging. It is usually addressed by highly sensitive PCR- or sequencing-based screening of specific mutations, or by multiparametric flow cytometry. However, not all patients have suitable mutations and heterogeneity of surface markers hampers standardization in clinical routine. In this study, we propose an alternative approach to estimate MRD based on AML-associated DNA methylation (DNAm) patterns. We identified four CG dinucleotides (CpGs) that commonly reveal aberrant DNAm in AML and their combination could reliably discern healthy and AML samples. Interestingly, bisulfite amplicon sequencing demonstrated that aberrant DNAm patterns were symmetric on both alleles, indicating that there is epigenetic crosstalk between homologous chromosomes. We trained shallow-learning and deep-learning algorithms to identify anomalous DNAm patterns. The method was then tested on follow-up samples with and without MRD. Notably, even samples that were classified as MRD negative often revealed higher anomaly ratios than healthy controls, which may reflect clonal hematopoiesis. Our results demonstrate that targeted DNAm analysis facilitates reliable discrimination of malignant and healthy samples. However, since healthy samples also comprise few abnormal-classified DNAm reads the approach does not yet reliably discriminate MRD positive and negative samples.

scholarly journals Exploring DNA Methylation Diversity in the Honey Bee Brain by Ultra-Deep Amplicon Sequencing

Epigenomes ◽  
2020 ◽  
Vol 4 (2) ◽  
pp. 10
Author(s):  
Robert Kucharski ◽  
Ryszard Maleszka
Keyword(s):  
Dna Methylation ◽  
Honey Bee ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Cell Types ◽  
Significant Loss ◽  
Frequent Patterns ◽  
Bisulphite Sequencing ◽  
Special Challenge ◽  
Methylation Patterns

Understanding methylation dynamics in organs or tissues containing many different cell types is a challenging task that cannot be efficiently addressed by the low-depth bisulphite sequencing of DNA extracted from such sources. Here we explored the feasibility of ultra-deep bisulphite sequencing of long amplicons to reveal the brain methylation patterns in three selected honey bee genes analysed across five distinct conditions on the Illumina MiSeq platform. By combing 15 libraries in one run we achieved a very high sequencing depth of 240,000–340,000 reads per amplicon, suggesting that most of the cell types in the honey bee brain, containing approximately 1 million neurons, are represented in this dataset. We found a small number of gene-specific patterns for each condition in individuals of different ages and performing distinct tasks with 80–90% of those were represented by no more than a dozen patterns. One possibility is that such a small number of frequent patterns is the result of differentially methylated epialleles, whereas the rare and less frequent patterns reflect activity-dependent modifications. The condition-specific methylation differences within each gene appear to be position-dependent with some CpGs showing significant changes and others remaining stable in a methylated or non-methylated state. Interestingly, no significant loss of methylation was detected in very old individuals. Our findings imply that these diverse patterns represent a special challenge in the analyses of DNA methylation in complex tissues and organs that cannot be investigated by low-depth genome-wide bisulphite sequencing. We conclude that ultra-deep sequencing of gene-specific amplicons combined with genotyping of differentially methylated epialleles is an effective way to facilitate more advanced neuro-epigenomic studies in honey bees and other insects.

scholarly journals DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Julia Franzen ◽  
Theodoros Georgomanolis ◽  
Anton Selich ◽  
Chao-Chung Kuo ◽  
Reinhard Stöger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Amplicon Sequencing ◽  
Cell Types ◽  
Ctcf Binding ◽  
Long Term Culture ◽  
Pattern Development ◽  
Genomic Regions ◽  
Cg Dinucleotides

AbstractCulture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift.

scholarly journals Cyclophilin A is a mitochondrial factor that forms antiapoptotic complexes with p23

2020 ◽  
Author(s):  
Cristina Daneri-Becerra ◽  
Brenda Valeiras ◽  
Mariana Lagadari ◽  
Mario D. Galigniana
Keyword(s):  
Signal Transduction ◽  
Heat Shock ◽  
Molecular Chaperone ◽  
Intracellular Trafficking ◽  
Functional Unit ◽  
Cyclophilin A ◽  
Cell Types ◽  
Cellular Processes ◽  
Murine Liver ◽  
High Level

AbstractCyclophilin A (CyPA) is an abundant and ubiquitously expressed protein belonging to the immunophilin family that has intrinsic peptidyl-prolyl-(cis/trans)-isomerase enzymatic activity. In addition to mediating the immunosuppressive effects of the drug cyclosporine A, CyPA is involved in multiple cellular processes such as protein folding, intracellular trafficking, signal transduction, and transcriptional regulation. Because CyPA is also a molecular chaperone, its expression is induced by several stressor agents and is a highly abundant protein in cancer cells. In this study, it is demonstrated that in several cell types and at least in murine liver, a significant pool of this immunophilin is primarily an intramitochondrial factor that migrates to the nucleus upon the onset of stress. It is also shown that CyPA has antiapoptotic action. Importantly, the capability of CyPA to form complexes with the small acidic cochaperone p23 is proven, this interaction being independent of the usual association of p23 with the heat-shock protein of 90-kDa, Hsp90. Furthermore, it is demonstrated that the CyPA•p23 complex enhances the antiapoptotic response of the cell, suggesting that both proteins form a functional unit whose high level of expression plays a significant role in cell survival.

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 Mitochondrial Glucocorticoid Receptors and Their Actions

2021 ◽  
Vol 22 (11) ◽  
pp. 6054
Author(s):  
Ioanna Kokkinopoulou ◽  
Paraskevi Moutsatsou
Keyword(s):  
Gene Expression ◽  
Glucocorticoid Receptors ◽  
Mitochondrial Gene ◽  
Cell Types ◽  
Ros Generation ◽  
Mitochondrial Gene Expression ◽  
Mitochondrial Energy Metabolism ◽  
Bcl2 Family ◽  
Cellular Processes ◽  
Almost All

Mitochondria are membrane organelles present in almost all eukaryotic cells. In addition to their well-known role in energy production, mitochondria regulate central cellular processes, including calcium homeostasis, Reactive Oxygen Species (ROS) generation, cell death, thermogenesis, and biosynthesis of lipids, nucleic acids, and steroid hormones. Glucocorticoids (GCs) regulate the mitochondrially encoded oxidative phosphorylation gene expression and mitochondrial energy metabolism. The identification of Glucocorticoid Response Elements (GREs) in mitochondrial sequences and the detection of Glucocorticoid Receptor (GR) in mitochondria of different cell types gave support to hypothesis that mitochondrial GR directly regulates mitochondrial gene expression. Numerous studies have revealed changes in mitochondrial gene expression alongside with GR import/export in mitochondria, confirming the direct effects of GCs on mitochondrial genome. Further evidence has made clear that mitochondrial GR is involved in mitochondrial function and apoptosis-mediated processes, through interacting or altering the distribution of Bcl2 family members. Even though its exact translocation mechanisms remain unknown, data have shown that GR chaperones (Hsp70/90, Bag-1, FKBP51), the anti-apoptotic protein Bcl-2, the HDAC6- mediated deacetylation and the outer mitochondrial translocation complexes (Tom complexes) co-ordinate GR mitochondrial trafficking. A role of mitochondrial GR in stress and depression as well as in lung and hepatic inflammation has also been demonstrated.

scholarly journals Differential Expression of Serum Exosome microRNAs and Cytokines in Influenza A and B Patients Collected in the 2016 and 2017 Influenza Seasons

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 149
Author(s):  
Sreekumar Othumpangat ◽  
William G. Lindsley ◽  
Donald H. Beezhold ◽  
Michael L. Kashon ◽  
Carmen N. Burrell ◽  
...  
Keyword(s):  
Healthy Volunteers ◽  
Influenza A ◽  
Influenza Infection ◽  
Cell Types ◽  
Airway Epithelial Cells ◽  
Differentially Expressed ◽  
Influenza B ◽  
Airway Epithelial ◽  
Monocyte Chemoattractant Protein 1 ◽  
Novel Approach

MicroRNAs (miRNAs) have remarkable stability and are key regulators of mRNA transcripts for several essential proteins required for the survival of cells and replication of the virus. Exosomes are thought to play an essential role in intercellular communications by transporting proteins and miRNAs, making them ideal in the search for biomarkers. Evidence suggests that miRNAs are involved in the regulation of influenza virus replication in many cell types. During the 2016 and 2017 influenza season, we collected blood samples from 54 patients infected with influenza and from 30 healthy volunteers to identify the potential role of circulating serum miRNAs and cytokines in influenza infection. Data comparing the exosomal miRNAs in patients with influenza B to healthy volunteers showed 76 miRNAs that were differentially expressed (p < 0.05). In contrast, 26 miRNAs were differentially expressed between patients with influenza A (p < 0.05) and the controls. Of these miRNAs, 11 were commonly expressed in both the influenza A and B patients. Interferon (IFN)-inducing protein 10 (IP-10), which is involved in IFN synthesis during influenza infection, showed the highest level of expression in both influenza A and B patients. Influenza A patients showed increased expression of IFNα, GM-CSF, interleukin (IL)-13, IL-17A, IL-1β, IL-6 and TNFα, while influenza B induced increased levels of EGF, G-CSF, IL-1α, MIP-1α, and TNF-β. In addition, hsa-miR-326, hsa-miR-15b-5p, hsa-miR-885, hsa-miR-122-5p, hsa-miR-133a-3p, and hsa-miR-150-5p showed high correlations to IL-6, IL-15, IL-17A, IL-1β, and monocyte chemoattractant protein-1 (MCP-1) with both strains of influenza. Next-generation sequencing studies of H1N1-infected human lung small airway epithelial cells also showed similar pattern of expression of miR-375-5p, miR-143-3p, 199a-3p, and miR-199a-5p compared to influenza A patients. In summary, this study provides insights into the miRNA profiling in both influenza A and B virus in circulation and a novel approach to identify the early infections through a combination of cytokines and miRNA expression.

scholarly journals Towards a contemporary player learning in development framework for sports practitioners

2021 ◽  
pp. 174795412110023
Author(s):  
Mark O Sullivan ◽  
Carl T Woods ◽  
James Vaughan ◽  
Keith Davids
Keyword(s):  
Linear Process ◽  
Task Environment ◽  
Coach Education ◽  
Development Framework ◽  
Novel Approach ◽  
Non Linear ◽  
And Performance ◽  
Learning Development ◽  
High Level ◽  
User Friendly

As it is appreciated that learning is a non-linear process – implying that coaching methodologies in sport should be accommodative – it is reasonable to suggest that player development pathways should also account for this non-linearity. A constraints-led approach (CLA), predicated on the theory of ecological dynamics, has been suggested as a viable framework for capturing the non-linearity of learning, development and performance in sport. The CLA articulates how skills emerge through the interaction of different constraints (task-environment-performer). However, despite its well-established theoretical roots, there are challenges to implementing it in practice. Accordingly, to help practitioners navigate such challenges, this paper proposes a user-friendly framework that demonstrates the benefits of a CLA. Specifically, to conceptualize the non-linear and individualized nature of learning, and how it can inform player development, we apply Adolph’s notion of learning IN development to explain the fundamental ideas of a CLA. We then exemplify a learning IN development framework, based on a CLA, brought to life in a high-level youth football organization. We contend that this framework can provide a novel approach for presenting the key ideas of a CLA and its powerful pedagogic concepts to practitioners at all levels, informing coach education programs, player development frameworks and learning environment designs in sport.

scholarly journals Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Todd R. Robeck ◽  
Zhe Fei ◽  
Ake T. Lu ◽  
Amin Haghani ◽  
Eve Jourdain ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Age Estimation ◽  
Species Conservation ◽  
Genome Wide ◽  
Epigenetic Aging ◽  
Highly Correlated ◽  
Methylation Patterns ◽  
Cg Dinucleotides ◽  
Free Ranging ◽  
Unique Species

AbstractThe development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies for wild odontocetes. Therefore, we determined genome-wide DNA methylation profiles using a custom array (HorvathMammalMethyl40) across skin and blood samples (n = 446) from known age animals representing nine odontocete species within 4 phylogenetic families to identify age associated CG dinucleotides (CpGs). The top CpGs were used to create a cross-validated OEAC clock which was highly correlated for individuals (r = 0.94) and for unique species (median r = 0.93). Finally, we applied the OEAC for estimating the age and sex of 22 wild Norwegian killer whales. DNA methylation patterns of age associated CpGs are highly conserved across odontocetes. These similarities allowed us to develop an odontocete epigenetic aging clock (OEAC) which can be used for species conservation efforts by provide a mechanism for estimating the age of free ranging odontocetes from either blood or skin samples.

Sign in / Sign up

Export Citation Format

Share Document