@article{BeckerKucharskiRoessleretal.2016, author = {Becker, Nils and Kucharski, Robert and R{\"o}ssler, Wolfgang and Maleszka, Ryszard}, title = {Age-dependent transcriptional and epigenomic responses to light exposure in the honey bee brain}, series = {FEBS Open Bio}, volume = {6}, journal = {FEBS Open Bio}, number = {7}, doi = {10.1002/2211-5463.12084}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147080}, pages = {622-639}, year = {2016}, abstract = {Light is a powerful environmental stimulus of special importance in social honey bees that undergo a behavioral transition from in-hive to outdoor foraging duties. Our previous work has shown that light exposure induces structural neuronal plasticity in the mushroom bodies (MBs), a brain center implicated in processing inputs from sensory modalities. Here, we extended these analyses to the molecular level to unravel light-induced transcriptomic and epigenomic changes in the honey bee brain. We have compared gene expression in brain compartments of 1- and 7-day-old light-exposed honey bees with age-matched dark-kept individuals. We have found a number of differentially expressed genes (DEGs), both novel and conserved, including several genes with reported roles in neuronal plasticity. Most of the DEGs show age-related changes in the amplitude of light-induced expression and are likely to be both developmentally and environmentally regulated. Some of the DEGs are either known to be methylated or are implicated in epigenetic processes suggesting that responses to light exposure are at least partly regulated at the epigenome level. Consistent with this idea light alters the DNA methylation pattern of bgm, one of the DEGs affected by light exposure, and the expression of microRNA miR-932. This confirms the usefulness of our approach to identify candidate genes for neuronal plasticity and provides evidence for the role of epigenetic processes in driving the molecular responses to visual stimulation.}, language = {en} } @article{CarmelaVeglianteRoyoPalomeroetal.2011, author = {Carmela Vegliante, Maria and Royo, Cristina and Palomero, Jara and Salaverria, Itziar and Balint, Balazs and Martin-Guerrero, Idoia and Agirre, Xabier and Lujambio, Amaia and Richter, Julia and Xargay-Torrent, Silvia and Bea, Silvia and Hernandez, Luis and Enjuanes, Anna and Jose Calasanz, Maria and Rosenwald, Andreas and Ott, German and Roman-Gomez, Jose and Prosper, Felipe and Esteller, Manel and Jares, Pedro and Siebert, Reiner and Campo, Elias and Martin-Subero, Jose I. and Amador, Virginia}, title = {Epigenetic Activation of SOX11 in Lymphoid Neoplasms by Histone Modifications}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {6}, doi = {10.1371/journal.pone.0021382}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-135325}, pages = {e21382}, year = {2011}, abstract = {Recent studies have shown aberrant expression of SOX11 in various types of aggressive B-cell neoplasms. To elucidate the molecular mechanisms leading to such deregulation, we performed a comprehensive SOX11 gene expression and epigenetic study in stem cells, normal hematopoietic cells and different lymphoid neoplasms. We observed that SOX11 expression is associated with unmethylated DNA and presence of activating histone marks (H3K9/14Ac and H3K4me3) in embryonic stem cells and some aggressive B-cell neoplasms. In contrast, adult stem cells, normal hematopoietic cells and other lymphoid neoplasms do not express SOX11. Such repression was associated with silencing histone marks H3K9me2 and H3K27me3. The SOX11 promoter of non-malignant cells was consistently unmethylated whereas lymphoid neoplasms with silenced SOX11 tended to acquire DNA hypermethylation. SOX11 silencing in cell lines was reversed by the histone deacetylase inhibitor SAHA but not by the DNA methyltransferase inhibitor AZA. These data indicate that, although DNA hypermethylation of SOX11 is frequent in lymphoid neoplasms, it seems to be functionally inert, as SOX11 is already silenced in the hematopoietic system. In contrast, the pathogenic role of SOX11 is associated with its de novo expression in some aggressive lymphoid malignancies, which is mediated by a shift from inactivating to activating histone modifications.}, language = {en} } @article{deNijsChoeSteinbuschetal.2019, author = {de Nijs, Laurence and Choe, Kyonghwan and Steinbusch, Hellen and Schijns, Olaf E. M. G. and Dings, Jim and van den Hove, Daniel L. A. and Rutten, Bart P. F. and Hoogland, Govert}, title = {DNA methyltransferase isoforms expression in the temporal lobe of epilepsy patients with a history of febrile seizures}, series = {Clinical Epigenetics}, volume = {11}, journal = {Clinical Epigenetics}, doi = {10.1186/s13148-019-0721-2}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223636}, year = {2019}, abstract = {Background Temporal lobe epilepsy (TLE) with hippocampal sclerosis (HS) is a common pharmaco-resistant epilepsy referred for adult epilepsy surgery. Though associated with prolonged febrile seizures (FS) in childhood, the neurobiological basis for this relationship is not fully understood and currently no preventive or curative therapies are available. DNA methylation, an epigenetic mechanism catalyzed by DNA methyltransferases (DNMTs), potentially plays a pivotal role in epileptogenesis associated with FS. In an attempt to start exploring this notion, the present cross-sectional pilot study investigated whether global DNA methylation levels (5-mC and 5-hmC markers) and DNMT isoforms (DNMT1, DNMT3a1, and DNMT3a2) expression would be different in hippocampal and neocortical tissues between controls and TLE patients with or without a history of FS. Results We found that global DNA methylation levels and DNMT3a2 isoform expression were lower in the hippocampus for all TLE groups when compared to control patients, with a more significant decrease amongst the TLE groups with a history of FS. Interestingly, we showed that DNMT3a1 expression was severely diminished in the hippocampus of TLE patients with a history of FS in comparison with control and other TLE groups. In the neocortex, we found a higher expression of DNMT1 and DNMT3a1 as well as increased levels of global DNA methylation for all TLE patients compared to controls. Conclusion Together, the findings of this descriptive cross-sectional pilot study demonstrated brain region-specific changes in DNMT1 and DNMT3a isoform expression as well as global DNA methylation levels in human TLE with or without a history of FS. They highlighted a specific implication of DNMT3a isoforms in TLE after FS. Therefore, longitudinal studies that aim at targeting DNMT3a isoforms to evaluate the potential causal relationship between FS and TLE or treatment of FS-induced epileptogenesis seem warranted.}, language = {en} } @article{DeekenGohlkeScholzetal.2013, author = {Deeken, Rosalia and Gohlke, Jochen and Scholz, Claus-Juergen and Kneitz, Susanne and Weber, Dana and Fuchs, Joerg and Hedrich, Rainer}, title = {DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall Tumors}, series = {PLoS Genetics}, journal = {PLoS Genetics}, doi = {10.1371/journal.pgen.1003267}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96318}, year = {2013}, abstract = {Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA-encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown gall development is known to be accompanied by global changes in transcription, metabolite levels, and physiological processes. High levels of abscisic acid (ABA) in crown galls regulate expression of drought stress responsive genes and mediate drought stress acclimation, which is essential for wild-type-like tumor growth. An impact of epigenetic processes such as DNA methylation on crown gall development has been suggested; however, it has not yet been investigated comprehensively. In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. Bisulfite sequencing analysis revealed that the oncogenes Ipt, IaaH, and IaaM were unmethylated in crown galls. Nevertheless, the oncogenes were susceptible to siRNA-mediated methylation, which inhibited their expression and subsequently crown gall growth. Genome arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed a globally hypermethylated crown gall genome, while promoters were rather hypomethylated. Mutants with reduced non-CG methylation developed larger tumors than the wild-type controls, indicating that hypermethylation inhibits plant tumor growth. The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. Genes known to be transcriptionally inhibited by ABA and methylated in crown galls became promoter methylated upon treatment of A. thaliana with ABA. This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. In summary, our studies provide evidence that epigenetic processes regulate gene expression, physiological processes, and the development of crown gall tumors.}, language = {en} } @article{ElHajjDittrichBoecketal.2016, author = {El Hajj, Nady and Dittrich, Marcus and B{\"o}ck, Julia and Kraus, Theo F. J. and Nanda, Indrajit and M{\"u}ller, Tobias and Seidmann, Larissa and Tralau, Tim and Galetzka, Danuta and Schneider, Eberhard and Haaf, Thomas}, title = {Epigenetic dysregulation in the developing Down syndrome cortex}, series = {Epigenetics}, volume = {11}, journal = {Epigenetics}, number = {8}, doi = {10.1080/15592294.2016.1192736}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191239}, pages = {563-578}, year = {2016}, abstract = {Using Illumina 450K arrays, 1.85\% of all analyzed CpG sites were significantly hypermethylated and 0.31\% hypomethylated in fetal Down syndrome (DS) cortex throughout the genome. The methylation changes on chromosome 21 appeared to be balanced between hypo- and hyper-methylation, whereas, consistent with prior reports, all other chromosomes showed 3-11times more hyper- than hypo-methylated sites. Reduced NRSF/REST expression due to upregulation of DYRK1A (on chromosome 21q22.13) and methylation of REST binding sites during early developmental stages may contribute to this genome-wide excess of hypermethylated sites. Upregulation of DNMT3L (on chromosome 21q22.4) could lead to de novo methylation in neuroprogenitors, which then persists in the fetal DS brain where DNMT3A and DNMT3B become downregulated. The vast majority of differentially methylated promoters and genes was hypermethylated in DS and located outside chromosome 21, including the protocadherin gamma (PCDHG) cluster on chromosome 5q31, which is crucial for neural circuit formation in the developing brain. Bisulfite pyrosequencing and targeted RNA sequencing showed that several genes of PCDHG subfamilies A and B are hypermethylated and transcriptionally downregulated in fetal DS cortex. Decreased PCDHG expression is expected to reduce dendrite arborization and growth in cortical neurons. Since constitutive hypermethylation of PCDHG and other genes affects multiple tissues, including blood, it may provide useful biomarkers for DS brain development and pharmacologic targets for therapeutic interventions.}, language = {en} } @article{FiedlerHirschElHajjetal.2019, author = {Fiedler, David and Hirsch, Daniela and El Hajj, Nady and Yang, Howard H. and Hu, Yue and Sticht, Carsten and Nanda, Indrajit and Belle, Sebastian and Rueschoff, Josef and Lee, Maxwell P. and Ried, Thomas and Haaf, Thomas and Gaiser, Timo}, title = {Genome-wide DNA methylation analysis of colorectal adenomas with and without recurrence reveals an association between cytosine-phosphate-guanine methylation and histological subtypes}, series = {Genes, Chromosomes and Cancer}, volume = {58}, journal = {Genes, Chromosomes and Cancer}, number = {11}, doi = {10.1002/gcc.22787}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212676}, pages = {783 -- 797}, year = {2019}, abstract = {Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development, which may result in colorectal cancer (CRC). Although gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and nonrecurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set of formalin-fixed paraffin-embedded colorectal low-grade adenomas (n = 72) consisting of primary adenomas without and with recurrence (n = 59), recurrent adenomas (n = 10), and normal mucosa specimens (n = 3). We aimed to unveil differentially methylated CpG positions (DMPs) across the methylome comparing not only primary adenomas without recurrence vs primary adenomas with recurrence but also primary adenomas vs recurrent adenomas using the Illumina Human Methylation 450K BeadChip array. Unsupervised hierarchical clustering exhibited a significant association of methylation patterns with histological adenoma subtypes. No significant DMPs were identified comparing primary adenomas with and without recurrence. Despite that, a total of 5094 DMPs (false discovery rate <0.05; fold change >10\%) were identified in the comparisons of recurrent adenomas vs primary adenomas with recurrence (674; 98\% hypermethylated), recurrent adenomas vs primary adenomas with and without recurrence (241; 99\% hypermethylated) and colorectal adenomas vs normal mucosa (4179; 46\% hypermethylated). DMPs in cytosine-phosphate-guanine (CpG) islands were frequently hypermethylated, whereas open sea- and shelf-regions exhibited hypomethylation. Gene ontology analysis revealed enrichment of genes associated with the immune system, inflammatory processes, and cancer pathways. In conclusion, our methylation data could assist in establishing a more robust and reproducible histological adenoma classification, which is a prerequisite for improving surveillance guidelines.}, language = {en} } @article{GeyerChalmersMacKintoshetal.2013, author = {Geyer, Kathrin K. and Chalmers, Iain W. and MacKintosh, Neil and Hirst, Julie E. and Geoghegan, Rory and Badets, Mathieu and Brophy, Peter M. and Brehm, Klaus and Hoffmann, Karl F.}, title = {Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes}, series = {BMC Genomics}, volume = {14}, journal = {BMC Genomics}, number = {462}, issn = {1471-2164}, doi = {10.1186/1471-2164-14-462}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121892}, year = {2013}, abstract = {Background: The phylum Platyhelminthes (flatworms) contains an important group of bilaterian organisms responsible for many debilitating and chronic infectious diseases of human and animal populations inhabiting the planet today. In addition to their biomedical and veterinary relevance, some platyhelminths are also frequently used models for understanding tissue regeneration and stem cell biology. Therefore, the molecular (genetic and epigenetic) characteristics that underlie trophic specialism, pathogenicity or developmental maturation are likely to be pivotal in our continued studies of this important metazoan group. Indeed, in contrast to earlier studies that failed to detect evidence of cytosine or adenine methylation in parasitic flatworm taxa, our laboratory has recently defined a critical role for cytosine methylation in Schistosoma mansoni oviposition, egg maturation and ovarian development. Thus, in order to identify whether this epigenetic modification features in other platyhelminth species or is a novelty of S. mansoni, we conducted a study simultaneously surveying for DNA methylation machinery components and DNA methylation marks throughout the phylum using both parasitic and non-parasitic representatives. Results: Firstly, using both S. mansoni DNA methyltransferase 2 (SmDNMT2) and methyl-CpG binding domain protein (SmMBD) as query sequences, we illustrate that essential DNA methylation machinery components are well conserved throughout the phylum. Secondly, using both molecular (methylation specific amplification polymorphism, MSAP) and immunological (enzyme-linked immunoabsorbent assay, ELISA) methodologies, we demonstrate that representative species (Echinococcus multilocularis, Protopolystoma xenopodis, Schistosoma haematobium, Schistosoma japonicum, Fasciola hepatica and Polycelis nigra) within all four platyhelminth classes (Cestoda, Monogenea, Trematoda and 'Turbellaria') contain methylated cytosines within their genome compartments. Conclusions: Collectively, these findings provide the first direct evidence for a functionally conserved and enzymatically active DNA methylation system throughout the Platyhelminthes. Defining how this epigenetic feature shapes phenotypic diversity and development within the phylum represents an exciting new area of metazoan biology.}, language = {en} } @phdthesis{Gohlke2013, author = {Gohlke, Jochen}, title = {Die Rolle von DNA-Methylierungen in der Entwicklung und Physiologie vonAgrobacterium-induzierten Arabidopsis-Tumoren}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-77732}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2013}, abstract = {Agrobacterium tumefaciens ist ein pathogenes Bodenbakterium, welches nach Integration seiner T-DNA in das pflanzliche Genom die Bildung von tumorartigen Wucherungen, den sogenannten Wurzelhalsgallen, an einer Reihe unterschiedlicher Wirtspflanzen verursacht. Die Expression der T-DNA-codierten Onkogene resultiert in der Proliferation und Differenzierung der sogenannten Wurzelhalsgallen, einem Prozess, welcher mit weitreichenden transkriptionellen und physiologischen Ver{\"a}nderungen verbunden ist. F{\"u}r DNA-Methylierungen ist bekannt, dass diese zu Genexpressionsver{\"a}nderungen beitragen, welche neoplastisches Wachstum in S{\"a}ugetieren beg{\"u}nstigen. {\"U}ber die Funktion epigenetischer Prozesse f{\"u}r die Physiologie und Entwicklung pflanzlicher Tumore ist bisher hingegen wenig bekannt. Daher wurde in dieser Arbeit das Methylierungsmuster von Wurzelhalsgallen, welche an Arabidopsis thaliana induziert wurden, sowohl genomweit als auch auf Basis einzelner Gene bestimmt. Dabei zeigte sich, dass die Onkogene ipt, iaaH und iaaM welche mit der T-DNA ins Genom integriert werden und die Proliferation ausl{\"o}sen, im Tumorgewebe unmethyliert vorliegen. Dennoch sind die Onkogene empf{\"a}nglich gegen{\"u}ber epigenetischen Modifikationen, da die siRNA-vermittelte Methylierung sowohl ihre Transkription als auch das Tumorwachstum unterbindet. Eine genomweite Studie der DNA-Methylierungsmuster mittels Tiling-Array-Analysen von immunopr{\"a}zipitierter methylierter DNA zeigte ein global hypermethyliertes Tumor-Genom im Vergleich zum tumorfreien Sprossgewebe. Diese Beobachtungen stehen im Gegensatz zu den Methylierungsmustern der meisten S{\"a}uger-Tumore, welche typischerweise mit globaler Hypomethylierung und lokaler Hypermethylierung von Promotor-Sequenzen assoziiert sind. Im Unterschied dazu waren die Promoter-Sequenzen im Pflanzentumor eher hypomethyliert. Die Methylierungsunterschiede zwischen Wurzelhalsgallen und Sprossgewebe korrelierten mit transkriptionellen Ver{\"a}nderungen. Speziell Gene, welche in Entwicklungsprozessen und Zellteilung involviert sind, waren von Methylierungs{\"a}nderungen betroffen. Dies impliziert, dass insbesondere diese Prozesse epigenetisch kontrolliert werden. Die Methylierung von Genen, welche einer transkriptionellen Kontrolle durch ABA unterliegen, war durch eine ABA-Behandlung induzierbar. DNA-Methylierungen kontrollieren somit wahrscheinlich essenzielle physiologische Prozesse w{\"a}hrend der Tumorentwicklung wie beispielsweise die ABA-vermittelte Trockenstressanpassung. Arabidopsis-Mutanten, welche in Nicht-CG-Methylierungsprozessen beeintr{\"a}chtigt sind, entwickelten gr{\"o}ßere Tumore als die Kontrollpflanzen der entsprechenden Wildtypen. Dies weist auf eine Inhibierung des Tumor-Wachstums durch ein hypermethyliertes Genom, insbesondere der Nicht-CG-Motive hin. Insgesamt zeigen die Ergebnisse, dass Genexpression, physiologische Prozesse und die Entwicklung pflanzlicher Tumore einer Regulation durch DNA-Methylierung unterliegen.}, subject = {Abscisins{\"a}ure}, language = {de} } @article{HaertleElHajjDittrichetal.2017, author = {Haertle, Larissa and El Hajj, Nady and Dittrich, Marcus and M{\"u}ller, Tobias and Nanda, Indrajit and Lehnen, Harald and Haaf, Thomas}, title = {Epigenetic signatures of gestational diabetes mellitus on cord blood methylation}, series = {Clinical Epigenetics}, volume = {9}, journal = {Clinical Epigenetics}, number = {28}, doi = {10.1186/s13148-017-0329-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159459}, year = {2017}, abstract = {Background: Intrauterine exposure to gestational diabetes mellitus (GDM) confers a lifelong increased risk for metabolic and other complex disorders to the offspring. GDM-induced epigenetic modifications modulating gene regulation and persisting into later life are generally assumed to mediate these elevated disease susceptibilities. To identify candidate genes for fetal programming, we compared genome-wide methylation patterns of fetal cord bloods (FCBs) from GDM and control pregnancies. Methods and results: Using Illumina's 450K methylation arrays and following correction for multiple testing, 65 CpG sites (52 associated with genes) displayed significant methylation differences between GDM and control samples. Four candidate genes, ATP5A1, MFAP4, PRKCH, and SLC17A4, from our methylation screen and one, HIF3A, from the literature were validated by bisulfite pyrosequencing. The effects remained significant after adjustment for the confounding factors maternal BMI, gestational week, and fetal sex in a multivariate regression model. In general, GDM effects on FCB methylation were more pronounced in women with insulin-dependent GDM who had a more severe metabolic phenotype than women with dietetically treated GDM. Conclusions: Our study supports an association between maternal GDM and the epigenetic status of the exposed offspring. Consistent with a multifactorial disease model, the observed FCB methylation changes are of small effect size but affect multiple genes/loci. The identified genes are primary candidates for transmitting GDM effects to the next generation. They also may provide useful biomarkers for the diagnosis, prognosis, and treatment of adverse prenatal exposures.}, language = {en} } @article{HaertleMaierhoferBoecketal.2017, author = {Haertle, Larissa and Maierhofer, Anna and B{\"o}ck, Julia and Lehnen, Harald and B{\"o}ttcher, Yvonne and Bl{\"u}her, Matthias and Schorsch, Martin and Potabattula, Ramya and El Hajj, Nady and Appenzeller, Silke and Haaf, Thomas}, title = {Hypermethylation of the non-imprinted maternal MEG3 and paternal MEST alleles is highly variable among normal individuals}, series = {PLoS ONE}, volume = {12}, journal = {PLoS ONE}, number = {8}, doi = {10.1371/journal.pone.0184030}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170433}, pages = {e0184030}, year = {2017}, abstract = {Imprinted genes show parent-specific activity (functional haploidy), which makes them particularly vulnerable to epigenetic dysregulation. Here we studied the methylation profiles of oppositely imprinted genes at single DNA molecule resolution by two independent parental allele-specific deep bisulfite sequencing (DBS) techniques. Using Roche (GSJunior) next generation sequencing technology, we analyzed the maternally imprinted MEST promoter and the paternally imprinted MEG3 intergenic (IG) differentially methylated region (DMR) in fetal cord blood, adult blood, and visceral adipose tissue. Epimutations were defined as paternal or maternal alleles with >50\% aberrantly (de)methylated CpG sites, showing the wrong methylation imprint. The epimutation rates (range 2-66\%) of the paternal MEST and the maternal MEG3 IG DMR allele, which should be completely unmethylated, were significantly higher than those (0-15\%) of the maternal MEST and paternal MEG3 alleles, which are expected to be fully methylated. This hypermethylation of the non-imprinted allele (HNA) was independent of parental origin. Very low epimutation rates in sperm suggest that HNA occurred after fertilization. DBS with Illumina (MiSeq) technology confirmed HNA for the MEST promoter and the MEG3 IG DMR, and to a lesser extent, for the paternally imprinted secondary MEG3 promoter and the maternally imprinted PEG3 promoter. HNA leads to biallelic methylation of imprinted genes in a considerable proportion of normal body cells (somatic mosaicism) and is highly variable between individuals. We propose that during development and differentiation maintenance of differential methylation at most imprinting control regions may become to some extent redundant. The accumulation of stochastic and environmentally-induced methylation errors on the non-imprinted allele may increase epigenetic diversity between cells and individuals.}, language = {en} }