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 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 DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

2021 ◽  
Author(s):  
Carlos A. M. Cardoso-Junior ◽  
Boris Yagound ◽  
Isobel Ronai ◽  
Emily J. Remnant ◽  
Klaus Hartfelder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Honey Bee ◽  
Differential Gene Expression ◽  
Social Contexts ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Differential Gene ◽  
Honey Bee Workers ◽  
Methylation Patterns

AbstractIntragenic DNA methylation, also called gene body methylation, is an evolutionarily-conserved epigenetic mechanism in animals and plants. In social insects, gene body methylation is thought to contribute to behavioral plasticity, for example between foragers and nurse workers, by modulating gene expression. However, recent studies have suggested that the majority of DNA methylation is sequence-specific, and therefore cannot act as a flexible mediator between environmental cues and gene expression. To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen. Although these social contexts are known to bring about extreme changes in behavioral and reproductive traits through differential gene expression, we found no significant differences between the methylomes of workers from queenright and queenless colonies. In contrast, thousands of regions were differentially methylated between colonies, and these differences were not associated with differential gene expression in a subset of genes examined. Methylation patterns were highly similar between brain and ovary tissues and only differed in nine regions. These results strongly indicate that DNA methylation is not a driver of differential gene expression between tissues or behavioral morphs. Finally, despite the lack of difference in methylation patterns, queen presence affected the expression of all four DNA methyltransferase genes, suggesting that these enzymes have roles beyond DNA methylation. Therefore, the functional role of DNA methylation in social insect genomes remains an open question.

scholarly journals Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression

EBioMedicine ◽  
2019 ◽  
Vol 43 ◽  
pp. 411-423 ◽  
Author(s):  
Ewoud Ewing ◽  
Lara Kular ◽  
Sunjay J. Fernandes ◽  
Nestoras Karathanasis ◽  
Vincenzo Lagani ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Dna Methylation ◽  
Immune Cell ◽  
Cell Types ◽  
Combining Evidence ◽  
Methylation Patterns

scholarly journals Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage

2010 ◽  
Vol 21 (12) ◽  
pp. 2066-2077 ◽  
Author(s):  
Anita L. Sørensen ◽  
Bente Marie Jacobsen ◽  
Andrew H. Reiner ◽  
Ingrid S. Andersen ◽  
Philippe Collas
Keyword(s):  
Dna Methylation ◽  
Cell Types ◽  
Molecular Evidence ◽  
Mesenchymal Progenitors ◽  
H3k27 Methylation ◽  
Differentiated Cells ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
A Minor ◽  
Methylation Patterns

Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and developmental functions, whereas genes hypermethylated only in MSCs are associated with early development functions. We find that most lineage-specification promoters are DNA hypomethylated and harbor a combination of trimethylated H3K4 and H3K27, whereas early developmental genes are DNA hypermethylated with or without H3K27 methylation. Promoter DNA methylation patterns of differentiated cells are largely established at the progenitor stage; yet, differentiation segregates a minor fraction of the commonly hypermethylated promoters, generating greater epigenetic divergence between differentiated cell types than between their undifferentiated counterparts. We also show an effect of promoter CpG content on methylation dynamics upon differentiation and distinct methylation profiles on transcriptionally active and inactive promoters. We infer that methylation state of lineage-specific promoters in MSCs is not a primary determinant of differentiation capacity. Our results support the view of a common origin of mesenchymal progenitors.

scholarly journals Global Modulation in DNA Epigenetics during Pro-Inflammatory Macrophage Activation

2019 ◽  
Author(s):  
Nikhil Jain ◽  
Tamar Shahal ◽  
Tslil Gabrieli ◽  
Noa Gilat ◽  
Dmitry Torchinsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Single Molecule ◽  
Transcriptional Control ◽  
Excision Repair ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cell Types ◽  
Inflammatory Activation ◽  
Methylation Patterns

AbstractDNA methylation patterns create distinct gene expression profiles. These patterns are maintained after cell division, thus enabling the differentiation and maintenance of multiple cell types from the same genome sequence. The advantage of this mechanism for transcriptional control is that chemical-encoding allows to rapidly establish new epigenetic patterns “on-demand” through enzymatic methylation and de-methylation of DNA. Here we show that this feature is associated with the fast response of macrophages during their pro-inflammatory activation. By using a combination of mass spectroscopy and single-molecule imaging to quantify global epigenetic changes in the genomes of primary macrophages, we followed three distinct DNA marks (methylated, hydroxymethylated and unmethylated), involved in establishing new DNA methylation patterns during pro-inflammatory activation. The observed epigenetic modulation together with gene expression data generated for the involved enzymatic machinery, may suggest that de-methylation upon LPS-activation starts with oxidation of methylated CpGs, followed by excision-repair of these oxidized bases and their replacement with unmodified cytosine.

scholarly journals Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Haidan Yan ◽  
Dongwei Zhang ◽  
Hongbo Liu ◽  
Yanjun Wei ◽  
Jie Lv ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Human Cell ◽  
Cell Types ◽  
Chromatin Modifications ◽  
Methylation Patterns

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 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 Intergenerational transfer of DNA methylation marks in the honey bee

2020 ◽  
Vol 117 (51) ◽  
pp. 32519-32527 ◽  
Author(s):  
Boris Yagound ◽  
Emily J. Remnant ◽  
Gabriele Buchmann ◽  
Benjamin P. Oldroyd
Keyword(s):  
Dna Methylation ◽  
Honey Bee ◽  
Epigenetic Inheritance ◽  
Somatic Tissue ◽  
Methylation Profile ◽  
Evolutionary Significance ◽  
Evolutionary Potential ◽  
Mammalian Embryogenesis ◽  
Genome Bisulfite Sequencing ◽  
Methylation Patterns

The evolutionary significance of epigenetic inheritance is controversial. While epigenetic marks such as DNA methylation can affect gene function and change in response to environmental conditions, their role as carriers of heritable information is often considered anecdotal. Indeed, near-complete DNA methylation reprogramming, as occurs during mammalian embryogenesis, is a major hindrance for the transmission of nongenetic information between generations. Yet it remains unclear how general DNA methylation reprogramming is across the tree of life. Here we investigate the existence of epigenetic inheritance in the honey bee. We studied whether fathers can transfer epigenetic information to their daughters through DNA methylation. We performed instrumental inseminations of queens, each with four different males, retaining half of each male’s semen for whole genome bisulfite sequencing. We then compared the methylation profile of each father’s somatic tissue and semen with the methylation profile of his daughters. We found that DNA methylation patterns were highly conserved between tissues and generations. There was a much greater similarity of methylomes within patrilines (i.e., father-daughter subfamilies) than between patrilines in each colony. Indeed, the samples’ methylomes consistently clustered by patriline within colony. Samples from the same patriline had twice as many shared methylated sites and four times fewer differentially methylated regions compared to samples from different patrilines. Our findings indicate that there is no DNA methylation reprogramming in bees and, consequently, that DNA methylation marks are stably transferred between generations. This points to a greater evolutionary potential of the epigenome in invertebrates than there is in mammals.

scholarly journals Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma

2020 ◽  
Author(s):  
Lauren J. Mills ◽  
Milcah C. Scott ◽  
Pankti Shah ◽  
Anne R. Cunanan ◽  
Archana Deshpande ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Large Scale ◽  
Immune Cell ◽  
Cell Types ◽  
Structural Variations ◽  
Canine Osteosarcoma ◽  
Genome Wide ◽  
Highly Correlated ◽  
Murine Osteosarcoma ◽  
Methylation Patterns

AbstractOsteosarcoma is an aggressive tumor of the bone that primarily affects young adults and adolescents. Osteosarcoma is characterized by genomic chaos and heterogeneity. While inactivation of tumor suppressor p53 TP53 is nearly universal other high frequency mutations or structural variations have not been identified. Despite this genomic heterogeneity, key conserved transcriptional programs associated with survival have been identified across human, canine and induced murine osteosarcoma. The epigenomic landscape, including DNA methylation, plays a key role in establishing transcriptional programs in all cell types. The role of epigenetic dysregulation has been studied in a variety of cancers but has yet to be explored at scale in osteosarcoma. Here we examined genome-wide DNA methylation patterns in 24 human and 44 canine osteosarcoma samples identifying groups of highly correlated DNA methylation marks in human and canine osteosarcoma samples. We also link specific DNA methylation patterns to key transcriptional programs in both human and canine osteosarcoma. Building on previous work, we built a DNA methylation-based measure for the presence and abundance of various immune cell types in osteosarcoma. Finally, we determined that the underlying state of the tumor, and not changes in cell composition, were the main driver of differences in DNA methylation across the human and canine samples.SignificanceThis is the first large scale study of DNA methylation in osteosarcoma and lays the ground work for the exploration of DNA methylation programs that help establish conserved transcriptional programs in the context of different genomic landscapes.

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