Article
Plant Sciences
Ricardo Bianchetti, Nicolas Bellora, Luis A. de Haro, Rafael Zuccarelli, Daniele Rosado, Luciano Freschi, Magdalena Rossi, Luisa Bermudez
Summary: Phytochrome-mediated light and temperature perception plays an important role in regulating fruit development, ripening, and nutritional quality. This study reveals that the regulation of fruit development by Phytochrome involves epigenetic mechanisms, specifically DNA demethylation. The findings show that Phytochrome has a greater impact on the methylome and transcriptome of tomato fruits in the breaker stage compared to the immature green stage. Additionally, PHYB1B2 has a more substantial effect on ripening-associated methylation reprogramming. The study also uncovers a gene expression network involving chromatin organization factors and transcriptional regulators that mediate the PHYB1B2 signal transduction. These findings provide insights into how epigenetic mechanisms respond to environmental cues and affect agronomical traits.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Francesca Lucibelli, Maria Carmen Valoroso, Serena Aceto
Summary: DNA methylation is an epigenetic modification that regulates gene expression and chromatin structure in plant genomes. It plays a crucial role in plant development and evolution, as well as in plant responses to biotic and abiotic stress. Furthermore, DNA methylation has potential evolutionary implications and biotechnological applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Samuel N. Bogan, Marie E. Strader, Gretchen E. Hofmann
Summary: This study investigates the effects of DNA methylation on gene expression and splicing in the larvae of the purple sea urchin. It finds that differential gene body methylation has stronger effects on gene expression among genes with poorly accessible transcriptional start sites, and the baseline transcript abundance influences the direction of this effect. Considering the interactions between methylation and chromatin accessibility, the transcriptional responses to maternal conditioning are significantly increased, suggesting that the relationship between methylation and gene regulation is partially explained by chromatin state.
Article
Environmental Sciences
Thomas Sol Dourdin, Guillaume Riviere, Alexandre Cormier, Carole Di Poi, Killian Guyomard, Manuella Rabiller, Farida Akcha, Thierno Bah Sadialiou, Pauline Le Monier, Rossana Sussarellu
Summary: Early exposure to an environmentally relevant pesticide mixture induces multi-scale latent effects possibly affecting life history traits in the Pacific oyster, Crassostrea gigas. The study found that exposure to a combination of 18 pesticides and metals at environmental concentrations during the embryo-larval stage resulted in disturbed swimming behavior, increased size and weight at specific time points, and altered expression of development-related genes. Additionally, DNA methylation analyses showed significant modifications in exposed larvae, marked by a demethylation trend.
ENVIRONMENTAL POLLUTION
(2023)
Article
Genetics & Heredity
Ryan J. Corbett, Andrea M. Luttman, Kaitlin E. Wurtz, Janice M. Siegford, Nancy E. Raney, Laura M. Ford, Catherine W. Ernst
Summary: The weaning stress in piglets results in genome-wide methylation changes associated with differential gene expression, reduced T cell activation, and altered HPA axis response.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Aleksandra Gorska, Maria Urbanowicz, Lukasz Grochowalski, Michal Seweryn, Marta Sobalska-Kwapis, Tomasz Wojdacz, Magdalena Lange, Marta Gruchala-Niedoszytko, Justyna Jarczak, Dominik Strapagiel, Magdalena Gorska-Ponikowska, Iwona Pelikant-Malecka, Leszek Kalinowski, Boguslaw Nedoszytko, Danuta Gutowska-Owsiak, Marek Niedoszytko
Summary: This study aimed to identify the differential methylation profiles and gene expression patterns associated with mastocytosis, a heterogenous disease of the mast cells. Genome-wide DNA methylation analysis was performed on peripheral blood samples from mastocytosis patients and healthy controls. The results showed significant differences in methylation levels of selected regions, including 31 genes located within the regulatory regions. Additionally, three oncogenes-FOXQ1, TWIST1, and ERG-were found to be differentially methylated in mastocytosis patients for the first time. These findings provide insights into the methylation landscape of mastocytosis and potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Lei Lei, Xinxin Xu, Chengchen Gong, Bowen Lin, Fang Li
Summary: This study identified candidate genes of ovarian endometriosis through integrated analysis of genome-wide gene expression and DNA methylation profiles, revealing the significance of DNA methylation in gene expression.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Young-Dan Cho, Woo-Jin Kim, Sungtae Kim, Young Ku, Hyun-Mo Ryoo
Summary: The study found that the surface roughness of titanium implants affects their osteogenic potential, with sandblasted/large-grit/acid-etched (SLA) surfaces showing superior osteogenic response compared to machined surfaces, likely due to a different epigenetic landscape, particularly DNA methylation of the Alp gene.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Jessica Pazzaglia, Emanuela Dattolo, Miriam Ruocco, Alex Santillan-Sarmiento, Lazaro Marin-Guirao, Gabriele Procaccini
Summary: This study analyzed the dynamics of DNA methylation (DNAm) in marine plants in response to environmental changes. The results showed that temperature and nutrient conditions had significant effects on DNAm, highlighting the potential role of environmental factors in regulating species adaptation and phenotypic differences.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Sarbottam Piya, Valeria S. Lopes-Caitar, Won-Seok Kim, Vince Pantalone, Hari B. Krishnan, Tarek Hewezi
Summary: This study revealed that DNA methylation levels of miRNA genes were significantly higher in nodules compared with root tissues at different developmental stages. A total of 82 differentially methylated miRNAs were identified, with most being hypermethylated in nodules and showing stage-specific methylation patterns. Differentially methylated regions in the promoters of miRNAs overlapped with transposable elements, suggesting a potential explanation for the vulnerability of miRNAs to DNA methylation changes during nodule development. Gene expression analysis indicated a negative association between DNA methylation and miRNA expression, contributing to nodule development through indirect regulation of genes involved in cellular processes and pathways essential for nodulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Immunology
Dorota Iwaszkiewicz-Grzes, Magdalena Piotrowska, Mateusz Gliwinski, Zuzanna Urban-Wojciuk, Piotr Trzonkowski
Summary: The study revealed that insulin beta chain peptide 9-23 favored specific Tregs expression, while whole insulin activated both Tregs and Teffs. Tregs SPECB:9-23 showed the highest level of expression in crucial genes and lower methylation levels.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Evolutionary Biology
Jiao Wang, Xuyuan Liu, Yue Lan, Tengcheng Que, Jing Li, Bisong Yue, Zhenxin Fan
Summary: This study investigated the methylation patterns of Tibetan macaque, Chinese rhesus macaque, and crab-eating macaque, and compared the differences among them. The results showed differences in methylation and gene expression profiles among the three macaque species, which may be associated with variations in physiology and habitat. Additionally, a potential mechanism through which genomic alterations modulate methylation landscapes and influence the transcriptome was identified.
EVOLUTIONARY APPLICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Jacek Rysz, Beata Franczyk, Magdalena Rysz-Gorzynska, Anna Gluba-Brzozka
Summary: The modifications in genomic DNA methylation play a crucial role in regulating normal and pathological cellular processes, and are associated with the development of diseases such as atherogenesis, cancers, and chronic kidney disease (CKD). Altered DNA methylation can affect the progression of renal disease by modulating the expression of pro-inflammatory and pro-fibrotic genes, as well as genes essential for kidney development and function. Understanding the genetic-epigenetic profile is important for unraveling the processes underlying CKD development and improving the ability to identify individuals at risk and choose appropriate disease management.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Kira A. Perzel Mandell, Nicholas J. Eagles, Richard Wilton, Amanda J. Price, Stephen A. Semick, Leonardo Collado-Torres, Ran Tao, Shizhong Han, Alexander S. Szalay, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Summary: The study found that DNA methylation is influenced by genetic factors, with a significant portion of genes and regions being associated with SNPs and CpG sites, providing insights into the genetic susceptibility of schizophrenia. By uncovering regions of differential methylation caused by schizophrenia risk-SNPs, the research discusses the relevance of epigenetic plasticity in the brain.
NATURE COMMUNICATIONS
(2021)
Article
Pharmacology & Pharmacy
Md. Shahid Sarwar, David Cheng, Rebecca Mary Peter, Ahmad Shannar, Pochung Chou, Lujing Wang, Renyi Wu, Davit Sargsyan, Michael Goedken, Yujue Wang, Xiaoyang Su, Ronald P. Hart, Ah-Ng Kong
Summary: This study investigated the regulation of cellular metabolism, DNA methylation, and transcriptome status in the kidney of diabetic nephropathy mice under high glucose conditions. The results showed that high glucose regulated cellular metabolites, metabolic signaling pathways, gene expression, and DNA methylation, which may be involved in the progression of diabetic nephropathy.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2023)
