scholarly journals DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
John P. Thomson ◽  
Angie Fawkes ◽  
Raffaele Ottaviano ◽  
Jennifer M. Hunter ◽  
Ruchi Shukla ◽  
...  
Keyword(s):  
Rapid Method ◽  
Genome Wide ◽  
Semiconductor Sequencing ◽  
Epigenetic Signatures

scholarly journals Distinct epigenetic signatures between adult-onset and late-onset depression

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hirotaka Yamagata ◽  
Hiroyuki Ogihara ◽  
Koji Matsuo ◽  
Shusaku Uchida ◽  
Ayumi Kobayashi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Clinical Symptoms ◽  
Late Onset ◽  
Adult Onset ◽  
Blood Biomarkers ◽  
Major Depressive ◽  
Genome Wide ◽  
Healthy Control ◽  
Epigenetic Signatures

AbstractThe heterogeneity of major depressive disorder (MDD) is attributed to the fact that diagnostic criteria (e.g., DSM-5) are only based on clinical symptoms. The discovery of blood biomarkers has the potential to change the diagnosis of MDD. The purpose of this study was to identify blood biomarkers of DNA methylation by strategically subtyping patients with MDD by onset age. We analyzed genome-wide DNA methylation of patients with adult-onset depression (AOD; age ≥ 50 years, age at depression onset < 50 years; N = 10) and late-onset depression (LOD; age ≥ 50 years, age at depression onset ≥ 50 years; N = 25) in comparison to that of 30 healthy subjects. The methylation profile of the AOD group was not only different from that of the LOD group but also more homogenous. Six identified methylation CpG sites were validated by pyrosequencing and amplicon bisulfite sequencing as potential markers for AOD in a second set of independent patients with AOD and healthy control subjects (N = 11). The combination of three specific methylation markers achieved the highest accuracy (sensitivity, 64%; specificity, 91%; accuracy, 77%). Taken together, our findings suggest that DNA methylation markers are more suitable for AOD than for LOD patients.

scholarly journals Disease-associated DNA methylation signatures in esophageal biopsies of children diagnosed with Eosinophilic Esophagitis

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Caterina Strisciuglio ◽  
Felicity Payne ◽  
Komal Nayak ◽  
Marialuisa Andreozzi ◽  
Alessandra Vitale ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Eosinophilic Esophagitis ◽  
Field Potential ◽  
Line Treatment ◽  
Food Impaction ◽  
First Line ◽  
Genome Wide ◽  
Epigenetic Signatures ◽  
The Impact ◽  
First Line Treatment

AbstractEosinophilic esophagitis (EoE) is a leading cause of dysphagia and food impaction in children and adults. The diagnosis relies on histological examination of esophageal mucosal biopsies and requires the presence of > 15 eosinophils per high-powered field. Potential pitfalls include the impact of biopsy sectioning as well as regional variations of eosinophil density. We performed genome-wide DNA methylation analyses on 30 esophageal biopsies obtained from children diagnosed with EoE (n = 7) and matched controls (n = 13) at the time of diagnosis as well as following first-line treatment. Analyses revealed striking disease-associated differences in mucosal DNA methylation profiles in children diagnosed with EoE, highlighting the potential for these epigenetic signatures to be developed into clinically applicable biomarkers.

scholarly journals Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma

Epigenetics ◽  
2018 ◽  
Vol 13 (4) ◽  
pp. 432-448 ◽  
Author(s):  
Rajendra P. Pangeni ◽  
Zhou Zhang ◽  
Angel A. Alvarez ◽  
Xuechao Wan ◽  
Namratha Sastry ◽  
...  
Keyword(s):  
Stem Cells ◽  
Glioma Stem Cells ◽  
Genome Wide ◽  
Epigenetic Signatures

scholarly journals GENT-14. GENOME WIDE METHYLOMIC AND TRANSCRIPTOMIC ANALYSES IDENTIFY EPIGENETIC SIGNATURES UNIQUELY DYSREGULATED IN GBM SUBTYPES

2016 ◽  
Vol 18 (suppl_6) ◽  
pp. vi76-vi76
Author(s):  
Rajendra Pangeni ◽  
Angel Alvarez ◽  
Tianzhi Huang ◽  
Wei Zhang ◽  
Zhou Zhang ◽  
...  
Keyword(s):  
Genome Wide ◽  
Epigenetic Signatures

scholarly journals Novel multiple sclerosis susceptibility loci implicated in epigenetic regulation

2016 ◽  
Vol 2 (6) ◽  
pp. e1501678 ◽  
Author(s):  
Till F. M. Andlauer ◽  
Dorothea Buck ◽  
Gisela Antony ◽  
Antonios Bayas ◽  
Lukas Bechmann ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Genome Wide Association Study ◽  
Immune Cell ◽  
Susceptibility Loci ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Substructure ◽  
Epigenetic Signatures ◽  
Folate Cycle ◽  
Ms Pathogenesis

We conducted a genome-wide association study (GWAS) on multiple sclerosis (MS) susceptibility in German cohorts with 4888 cases and 10,395 controls. In addition to associations within the major histocompatibility complex (MHC) region, 15 non-MHC loci reached genome-wide significance. Four of these loci are novel MS susceptibility loci. They map to the genesL3MBTL3,MAZ,ERG, andSHMT1. The lead variant atSHMT1was replicated in an independent Sardinian cohort. Products of the genesL3MBTL3,MAZ, andERGplay important roles in immune cell regulation.SHMT1encodes a serine hydroxymethyltransferase catalyzing the transfer of a carbon unit to the folate cycle. This reaction is required for regulation of methylation homeostasis, which is important for establishment and maintenance of epigenetic signatures. Our GWAS approach in a defined population with limited genetic substructure detected associations not found in larger, more heterogeneous cohorts, thus providing new clues regarding MS pathogenesis.

scholarly journals Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells

2011 ◽  
Vol 21 (10) ◽  
pp. 1601-1615 ◽  
Author(s):  
L. Pirola ◽  
A. Balcerczyk ◽  
R. W. Tothill ◽  
I. Haviv ◽  
A. Kaspi ◽  
...  
Keyword(s):  
Vascular Cells ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Epigenetic Signatures

scholarly journals Genetic and epigenetic signatures associated with the rapid radiation of Aquilegia species

2019 ◽  
Author(s):  
Tianyuan Lu ◽  
Ming-Rui Li ◽  
Ning Ding ◽  
Zhen-Hui Wang ◽  
Li-Zhen Lan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Adaptive Radiation ◽  
North American ◽  
Model System ◽  
Epigenetic Factors ◽  
Epigenetic Variability ◽  
Species Diversification ◽  
Genome Wide ◽  
Cell Reproduction ◽  
Epigenetic Signatures

AbstractElucidating how the diverse evolutionary mechanisms interact to determine species diversification is crucial to understanding the evolution and persistence of biodiversity. The genus Aquilegia (columbine) is a model system to identify genetic and epigenetic signatures underpinning the rapid adaptive radiation. In this study, we surveyed the genomes and DNA methylomes of ten worldwide Aquilegia species to investigate whether specific genomic architectures were associated with rapid species diversification in the Asian, European and North American lineages. The resulting phylogenies and population structure inferences revealed clearly high genetic and DNA methylomic divergence among the three lineages. Genome-wide scanning demonstrated significantly higher positive and purifying selection pressures among the Asian species compared to the European and North American lineages. More importantly, candidate genes identified at the genetic and epigenetic levels are functionally related to diverse adaptation-related traits, such as stress tolerance, photosynthesis and cell reproduction. While a considerable proportion of the candidate genes share hotspots of intra- and inter-lineage divergence, genetic and epigenetic factors were found to act on complementary biological pathways. By assessing the interaction between genetic variations and epigenetic variability, we found that epigenetic variability is a partially independent factor that intertwines with genetic mechanism to facilitate the diversification of the Aquilegia species. Taken together, these findings suggest that specific genetic architectures have been involved in vital biological pathways in response to diverse environmental conditions and epigenetic modifications may play a complementary role in the process of adaptive speciation. Our study provides an exploratory overview of how the established genetic and epigenetic signatures are associated with the rapid species diversification of Aquilegia species.Author SummaryDisentangling the genetic and epigenetic bases underpinning species diversification is crucial to understanding the evolution and persistence of biodiversity. The columbine (genus Aquilegia) is a model system to address biological mechanisms associated with rapid adaptive radiation. We surveyed the genomes and DNA methylomes of ten worldwide columbine species to investigate whether specific genetic and epigenetic architectures were involved in the diversification of Asian, European and North American columbine species. We pinpointed candidate genes featuring rapid adaptive radiation identified at either the genetic or the epigenetic levels. These candidate genes are functionally associated with diverse adaptation-related traits such as cell reproduction, plant growth, and stress tolerance. Such genetic and epigenetic signatures have potential contributed adaptabilities to the columbine species to cope with diverse environmental conditions. In addition, we also showed that epigenetic modifications could act as a complementary factor that intertwined with genetic mechanism to facilitate the diversification of the columbine species. In all, our study provides a genome-wide view of how the genetic and epigenetic factors are associated with the rapid species diversification of the columbine species.

scholarly journals Genome-wide dysregulation of histone acetylation in the Parkinson’s disease brain

2019 ◽  
Author(s):  
Lilah Toker ◽  
Gia T Tran ◽  
Janani Sundaresan ◽  
Ole-Bjørn Tysnes ◽  
Guido Alves ◽  
...  
Keyword(s):  
Histone Acetylation ◽  
Chromatin Immunoprecipitation ◽  
Genetic Risk ◽  
Neurodegenerative Disorder ◽  
Unknown Etiology ◽  
Transcriptomic Data ◽  
Genome Wide ◽  
A Genome ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Epigenetic Signatures

AbstractParkinson disease (PD) is a complex neurodegenerative disorder of largely unknown etiology. While several genetic risk factors have been identified, the involvement of epigenetics in the pathophysiology of PD is mostly unaccounted for. We conducted a histone acetylome-wide association study in PD, using brain tissue from two independent cohorts of cases and controls. Immunoblotting revealed increased acetylation at several histone sites in PD, with the most prominent change observed for H3K27, a marker of active promoters and enhancers. Chromatin immunoprecipitation sequencing (ChIP-seq) further indicated that H3K27 hyperacetylation in the PD brain is a genome-wide phenomenon, with a strong predilection for genes implicated in the disease, including SNCA, PARK7, PRKN and MAPT. Integration of the ChIP-seq with transcriptomic data revealed that the correlation between promoter H3K27 acetylation and gene expression is attenuated in PD patients, suggesting that H3K27 acetylation may be decoupled from transcription in the PD brain. Our findings strongly suggest that dysregulation of histone acetylation plays an important role in the pathophysiology of PD and identify novel epigenetic signatures associated with the disease.

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