IntroductionAfter the success of polygenic risk scores (PRS) that embed a useful summary of genomic information in a comprehensive score, the wish to develop summary statistics for DNA methylation ...had become more pressing. Developing such a score faces challenges, as the score has to be specific and sensitive as well. Epidemiological research on DNA methylation and depression would benefit from such score.ObjectivesHere, we test a score trained on incident depression (case-control), i.e., a list of published weights for particular CpGs, for its validity in the context of depression severity as measured using MADRS in our sample with depressed patients only.MethodsDNA methylation was assessed using the Illumina Infinium MethylationEPIC 850k BeadChip on a sample of 119 patients with a diagnosis of MDD. After data cleaning, 113 participants were included in the analysis (Mage= 47 years, 57.98% women, MMADRS=27.7). Data processing was conducted using the RnBeads package. From the published reference for the overall sample, a list of 196 CpGs was provided, 170 of these were present in our dataset and used for the score. The list of non-smokers comprised 144 CpGs, of which 124 were available. The score per individual was built using M-values, using the formula: S(weight*DNA methylation value). The score was tested in association with depression and other typical confounders using multiple regression in R. Confounders included ancestry, BMI, age, sex, and 6 cell types. We tested both scores in our sample: smokers and non-smokers.ResultsIn contrast to our expectations, none of the regression analyses showed a significant association with depression (MADRS-score). Nonetheless, a significant association was seen with biological sex for both analysis (overall: p=0.036, non-smokers: p=0.026). A reduced model with only this predictor explained 5% and 4% of the variance of the summary score calculated (R2), respectively (overall: p=0.013; non-smokers: p=0.019). One of the ancestry components was marginally significant too in the non-smoker summary score (p=0.065). This was not the case anymore in the reduced model.ConclusionsOur results show that caution is still in place when using methylation risk scores as specificity and sensitivity might not yet be optimized. The score built for depression incidence does not seem fitting for depression severity at this moment. The use of DNA methylation, a marker that is generally sensitive to confounding factors, for a risk score, might pose more challenges in the context of reliable summary statistics, in particular also for cross-trait examination, which is currently a typical use of polygenic risk scores.Disclosure of InterestNone Declared
DNA methylation in plants Gallego-Bartolomé, Javier
New phytologist,
07/2020, Volume:
227, Issue:
1
Journal Article
Peer reviewed
Open access
DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been instrumental in the study of ...this mark in plants, although their genome-wide effect complicates the direct association between changes in methylation and a particular phenotype. A variety of tools that allow locus-specific manipulation of DNA methylation can be used to assess its direct role in specific processes, as well as to create novel epialleles. Recently, new tools that recruit the methylation machinery directly to target loci through programmable DNA-binding proteins have expanded the tool kit available to researchers. This review provides an overview of DNA methylation in plants and discusses the tools that have recently been developed for its manipulation.
ABSTRACT
Detailed understanding of molecular mechanisms controlling adipogenesis is of great importance to identify new targets for treating obesity. Emerging evidence suggests that long noncoding ...RNAs (lncRNAs) may play a pivotal role in adipogenesis. Here, we have identified a novel lncRNA, Plnc1, which is transcribed from a position ~25,000 bp upstream of the peroxisome proliferator‐activated receptor γ2(PPAR‐γ2) gene. Plnc1 is abundantly expressed in adipose tissue, and obese mice have higher Plnc1 expression in adipose tissue than nonobese mice. Plnc1 was induced in established adipogenic lines ST2, 3T3‐L1, and C3H10T1/2 as well as in bone marrow stromal cells (BMSCs) after adipogenic treatment. Plnc1 knockdown blocked differentiation of ST2 cells and BMSCs into mature adipocytes, along with the reduction of PPAR‐γ, CCAAT/enhancer binding protein‐α, and adipocyte protein 2. Conversely, overexpression of Plnc1 promoted ST2 cells and BMSCs to fully differentiate. Mechanism studies revealed that Plnc1 could reduce the methylation level of CpG region in the PPAR‐γ2 promoter and enhance the transcriptional activity of the promoter and thereby increase PPAR‐γ2 transcription. Our study suggests that Plnc1 promotes adipogenic differentiation through controlling the key adipogenic transcription factor PPAR‐g and highlights the potential of Plnc1 as a target for new therapies to control metabolic disorders like obesity.—Zhu, E., Zhang, J., Li, Y., Yuan, H., Zhou, J., Wang, B. Long noncoding RNA Plnc1 controls adipocyte differentiation by regulating peroxisome proliferator‐activated receptor γ. FASEB J. 33, 2396–2408 (2019). www.fasebj.org
Transposable elements (TEs) generate mutations and chromosomal instability when active. To repress TE activity, eukaryotic cells evolved mechanisms to both degrade TE mRNAs into small interfering ...RNAs (siRNAs) and modify TE chromatin to epigenetically inhibit transcription. Since the populations of small RNAs that participate in TE post‐transcriptional regulation differ from those that establish RNA‐directed DNA methylation (RdDM), the mechanism through which transcriptionally active TEs transition from post‐transcriptional RNAi regulation to chromatin level control has remained unclear. We have identified the molecular mechanism of a plant pathway that functions to direct DNA methylation to transcriptionally active TEs. We demonstrated that 21–22 nucleotide (nt) siRNA degradation products from the RNAi of TE mRNAs are directly incorporated into the ARGONAUTE 6 (AGO6) protein and direct AGO6 to TE chromatin to guide its function in RdDM. We find that this pathway functions in reproductive precursor cells to primarily target long centromeric high‐copy transcriptionally active TEs for RdDM prior to gametogenesis. This study provides a direct mechanism that bridges the gap between the post‐transcriptional regulation of TEs and the establishment of TE epigenetic silencing.
Synopsis
Transcriptional activation of transposable elements (TEs) in plants leads to initial mRNA destruction through RNAi. AGO6 incorporates the resulting siRNAs and induces DNA methylation at TE target loci, thus establishing de novo epigenetic silencing.
RNA‐directed DNA methylation targets transcriptionally active transposable elements
AGO6 incorporates 21–22nt siRNAs produced by RNAi from transposable element mRNAs
Transposon‐derived siRNAs target AGO6 to chromatin and direct de novo DNA methylation
AGO6 plays a dual role by maintaining epigenetic silencing and initiating establishment of repressive chromatin states
This mechanism bridges the worlds of post‐transcriptional and transcriptional gene silencing by linking mRNA degradation via RNAi to the establishment of DNA methylation
Transcriptional activation of transposable elements (TEs) in plants leads to initial mRNA destruction through RNAi. AGO6 incorporates the resulting siRNAs and induces DNA methylation at TE target loci, thus establishing de novo epigenetic silencing.
Transgenerational epigenetic inheritance in mammals remains a debated subject. Here, we demonstrate that DNA methylation of promoter-associated CpG islands (CGIs) can be transmitted from parents to ...their offspring in mice. We generated DNA methylation-edited mouse embryonic stem cells (ESCs), in which CGIs of two metabolism-related genes, the Ankyrin repeat domain 26 and the low-density lipoprotein receptor, were specifically methylated and silenced. DNA methylation-edited mice generated by microinjection of the methylated ESCs exhibited abnormal metabolic phenotypes. Acquired methylation of the targeted CGI and the phenotypic traits were maintained and transmitted across multiple generations. The heritable CGI methylation was subjected to reprogramming in parental PGCs and subsequently reestablished in the next generation at post-implantation stages. These observations provide a concrete step toward demonstrating transgenerational epigenetic inheritance in mammals, which may have implications in our understanding of evolutionary biology as well as the etiology, diagnosis, and prevention of non-genetically inherited human diseases.
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•Establishment of targeted CGI methylation editing in mouse ES cells•DNA methylation-edited mice exhibit phenotypic alterations induced by gene silencing•Both acquired methylation and phenotypes are transmitted across multiple generations•Heritable epigenetic memory reestablishes CGI methylation at the epiblast stage
Takahashi et al. demonstrate that engineered epigenetic modifications and associated phenotypes can be transmitted across multiple generations in mammals.
DNA methylation is a chemical modification that defines cell type and lineage through the control of gene expression and genome stability. Disruption of DNA methylation control mechanisms causes a ...variety of diseases, including cancer. Cancer cells are characterized by aberrant DNA methylation (i.e., genome-wide hypomethylation and site-specific hypermethylation), mainly targeting CpG islands in gene expression regulatory elements. In particular, the early findings that a variety of tumor suppressor genes (TSGs) are targets of DNA hypermethylation in cancer led to the proposal of a model in which aberrant DNA methylation promotes cellular oncogenesis through TSGs silencing. However, recent genome-wide analyses have revealed that this classical model needs to be reconsidered. In this review, we will discuss the molecular mechanisms of DNA methylation abnormalities in cancer as well as their therapeutic potential.
DNA methylation is an important epigenetic modification that defines the properties of cells. Genome-wide hypomethylation, as well as hypermethylation of CpG islands associated with tumor suppressor genes and developmental regulators, are characteristics of cancer cells.DNA methyltransferases normally exist in an inactive form and their localization and activation are regulated by interaction with unique histone modifications at DNA methylation sites.Changes in DNA methylation patterns associated with carcinogenesis progress gradually with cell proliferation. Genome-wide hypomethylation is found in DNA blocks called partially methylated domains (PMDs) and it frequently occurs in solo-WCGW sequences that have no nearby CpG sequences and are adjacent to A or C.CpG island methylation primarily targets promoters characterized by low gene expression marked by H3K27m3, with the replacement of histone modifications by DNA methylation ensuring more stable gene repression.
Hypermethylation of the promoters of tumour suppressor genes represses transcription of these genes, conferring growth advantages to cancer cells. How these changes arise is poorly understood. Here ...we show that the activity of oxygen-dependent ten-eleven translocation (TET) enzymes is reduced by tumour hypoxia in human and mouse cells. TET enzymes catalyse DNA demethylation through 5-methylcytosine oxidation. This reduction in activity occurs independently of hypoxia-associated alterations in TET expression, proliferation, metabolism, hypoxia-inducible factor activity or reactive oxygen species, and depends directly on oxygen shortage. Hypoxia-induced loss of TET activity increases hypermethylation at gene promoters in vitro. In patients, tumour suppressor gene promoters are markedly more methylated in hypoxic tumour tissue, independent of proliferation, stromal cell infiltration and tumour characteristics. Our data suggest that up to half of hypermethylation events are due to hypoxia, with these events conferring a selective advantage. Accordingly, increased hypoxia in mouse breast tumours increases hypermethylation, while restoration of tumour oxygenation abrogates this effect. Tumour hypoxia therefore acts as a novel regulator of DNA methylation.
Gain-of-function IDH mutations are initiating events that define major clinical and prognostic classes of gliomas. Mutant IDH protein produces a new onco-metabolite, 2-hydroxyglutarate, which ...interferes with iron-dependent hydroxylases, including the TET family of 5'-methylcytosine hydroxylases. TET enzymes catalyse a key step in the removal of DNA methylation. IDH mutant gliomas thus manifest a CpG island methylator phenotype (G-CIMP), although the functional importance of this altered epigenetic state remains unclear. Here we show that human IDH mutant gliomas exhibit hypermethylation at cohesin and CCCTC-binding factor (CTCF)-binding sites, compromising binding of this methylation-sensitive insulator protein. Reduced CTCF binding is associated with loss of insulation between topological domains and aberrant gene activation. We specifically demonstrate that loss of CTCF at a domain boundary permits a constitutive enhancer to interact aberrantly with the receptor tyrosine kinase gene PDGFRA, a prominent glioma oncogene. Treatment of IDH mutant gliomaspheres with a demethylating agent partially restores insulator function and downregulates PDGFRA. Conversely, CRISPR-mediated disruption of the CTCF motif in IDH wild-type gliomaspheres upregulates PDGFRA and increases proliferation. Our study suggests that IDH mutations promote gliomagenesis by disrupting chromosomal topology and allowing aberrant regulatory interactions that induce oncogene expression.
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