Article
Cell Biology
Patricia Gonzalez-Rodriguez, Mathilde Cheray, Jens Fullgrabe, Maria Salli, Pinelopi Engskog-Vlachos, Lily Keane, Virginia Cunha, Agata Lupa, Wenbo Li, Qi Ma, Kristian Dreij, Michael G. Rosenfeld, Bertrand Joseph
Summary: Autophagy is a catabolic pathway that maintains cellular homeostasis and can be stimulated under cellular stress. The persistent downregulation of MAP1LC3 expression upon autophagy induction indicates an epigenetic memory of autophagy, offering insights into its long-term effects.
Article
Biochemistry & Molecular Biology
Jie Wang, Dandan Li, Jing Yang, Lu Chang, Rui Zhang, Jinming Li
Summary: This study utilized CRISPR/Cas9-mediated homology-directed repair pathway to achieve targeted editing of DNA methylation for gene silencing. By optimizing the method, the insertion efficiency was significantly improved, promoting stable methylation alterations through epigenetic recombination after cell division. The study confirmed that CRISPR/Cas9-mediated site-specific target methylation enables gene silencing to be maintained in vitro and in vivo.
Article
Biology
Carlos Ruiz-Arenas, Carles Hernandez-Ferrer, Marta Vives-Usano, Sergi Mari, Ines Quintela, Dan Mason, Solene Cadiou, Maribel Casas, Sandra Andrusaityte, Kristine Bjerve Gutzkow, Marina Vafeiadi, John Wright, Johanna Lepeule, Regina Grazuleviciene, Leda Chatzi, Angel Carracedo, Xavier Estivill, Eulalia Marti, Georgia Escaramis, Martine Vrijheid, Juan R. Gonzalez, Mariona Bustamante
Summary: This study identified autosomal cis eQTMs in children's blood by analyzing the relationship between DNA methylation levels and gene expression. These findings contribute to the interpretation of epigenome-wide association studies and provide a publicly available catalogue.
Article
Genetics & Heredity
Y. Feng, S. Cirera, E. Tasoz, Y. Liu, L. H. Olsen, B. O. Christoffersen, H. D. Pedersen, T. P. Ludvigsen, R. K. Kirk, C. Schumacher-Petersen, Y. Deng, M. Fredholm, F. Gao
Summary: The study found that Gottingen minipigs become morbidly obese on a high fat/fructose/cholesterol diet, and reversing their diet to a standard one can reverse lipid-related metabolic parameters. Differences were identified in the methylation patterning of promoters between the feeding groups, leading to dysregulation of metabolically-related genes. The potential of exploring diet-epigenome interactions for treating obesity was highlighted through this research.
FRONTIERS IN GENETICS
(2021)
Review
Environmental Sciences
D. Mahna, S. Puri, S. Sharma
Summary: Pesticides, widely used environmental contaminants, have been shown to have acute and chronic toxic effects on health. Research suggests that pesticides may induce DNA methylation modifications, potentially contributing to health issues in humans.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2021)
Article
Oncology
Debora D'Angelo Papaiz, Flavia Eichemberger Rius, Ana Luisa Pedroso Ayub, Clarice S. Origassa, Hemant Gujar, Diogo de Oliveira Pessoa, Eduardo Moraes Reis, Jeremie Nsengimana, Julia Newton-Bishop, Christopher E. Mason, Daniel J. Weisenberger, Gangning Liang, Miriam Galvonas Jasiulionis
Summary: In addition to mutations, epigenetic alterations contribute significantly to malignant transformation and tumor progression. By analyzing the methylome and transcriptome data, this study identified the relationship between changes in promoter and/or gene body DNA methylation and gene expression during different stages of melanoma progression. Two genes, Adcy3 and Inpp4b, were found to affect tumor growth and metastasis. The findings were validated by comparing them with clinical data from primary melanoma cohorts, suggesting potential prognostic markers.
MOLECULAR ONCOLOGY
(2022)
Article
Biochemical Research Methods
Wubin Ding, Diljeet Kaur, Steve Horvath, Wanding Zhou
Summary: Researchers have developed informatics infrastructure and methods for DNA methylation analysis in multiple species, including domesticated animals and laboratory mice. They have created a data-driven analysis pipeline for species inference, genome-specific data preprocessing, and regression modeling. Comparative analysis has revealed the dynamics of epigenome evolution in different genomic territories and tissue types, and specific methylation differences related to mouse strain phenotypes have been identified. These methods expand epigenome research to a wide range of species by streamlining DNA methylation array analysis for undesigned genomes.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Eshaan Patnaik, Chikezie Madu, Yi Lu
Summary: Epigenetics plays a crucial role in gene regulation and tumor development. DNA methylation inhibitors and histone deacetylase inhibitors can restore normal gene expression and be effective against cancer. Understanding epigenetic modifications and utilizing inhibitors offer new possibilities for cancer research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Simeon Santourlidis, Wolfgang A. Schulz, Marcos J. Arauzo-Bravo, Daniela Gerovska, Pauline Ott, Marcelo L. Bendhack, Mohamed Hassan, Lars Erichsen
Summary: Epigenetic mechanisms play a fundamental role in the initiation and development of melanoma, but research in this area is relatively limited compared to other cancers. This review provides a brief summary of the epigenetic aspects relevant to melanoma pathogenesis and introduces new perspectives from epigenetic research in other cancers that may have potential for melanoma diagnosis and therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Environmental Sciences
Maja Srut
Summary: The effect of environmental pollutants on epigenetic changes, including DNA methylation, histone modifications, and non-coding RNAs, is a major concern in ecotoxicology. Earthworms have been widely used as models to study the impact of environmental stress on epigenetic mechanisms and to explore the possibility of epigenetic inheritance. However, there are still many knowledge gaps that need to be filled in.
Article
Environmental Sciences
Arce Domingo-Relloso, Anne Bozack, Samara Kiihl, Zulema Rodriguez-Hernandez, Pilar Rentero-Garrido, J. Antonio Casasnovas, Montserrat Leon-Latre, Tamara Garcia-Barrera, J. Luis Gomez-Ariza, Belen Moreno, Ana Cenarro, Griselda de Marco, Faruque Parvez, Abu B. Siddique, Hasan Shahriar, Mohammad N. Uddin, Tariqul Islam, Ana Navas-Acien, Mary Gamble, Maria Tellez-Plaza
Summary: The study identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, but differences in As-related epigenetic sites across the study populations may also reflect low and high As-specific associations. This work contributes to a deeper understanding of potential epigenetic dysregulations of As, with further research needed to confirm biological consequences associated with DIP2C epigenetic regulation and investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.
ENVIRONMENTAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Zhenhui Zhong, Suhua Feng, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolom, Wanlu Liu, Steven E. Jacobsen
Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Harry MacKay, Chathura J. Gunasekara, Kit-Yi Yam, Dollada Srisai, Hari Krishna Yalamanchili, Yumei Li, Rui Chen, Cristian Coarfa, Robert A. Waterland
Summary: Recent studies have confirmed that obesity is primarily a neurodevelopmental disease influenced by nutrition during critical ontogenic windows. This study examines the role of epigenetic mechanisms in establishing and maintaining the brain's energy balance circuitry, specifically in the hypothalamic arcuate nucleus. The results indicate that postnatal epigenetic maturation is cell type and sex specific, occurring in genomic regions associated with body mass index heritability. These findings provide valuable insights into the limited ontogenic windows for developmental programming of obesity and the sex differences in sensitivity, and offer a resource for epigenetic analysis of energy balance programming.
Article
Evolutionary Biology
Aline M. Muyle, Danelle K. Seymour, Yuanda Lv, Bruno Huettel, Brandon S. Gaut
Summary: Gene body methylation in plants is an epigenetic mark that may be shaped by adaptation. This review discusses the establishment and maintenance of gene body methylation, as well as its potential roles in stabilizing and upregulating gene expression, inhibiting aberrant transcription, preventing intron retention, and protecting against transposable element insertions. While evidence supports a correlation between gene body methylation and gene expression patterns, it remains unclear if this relationship is causal.
GENOME BIOLOGY AND EVOLUTION
(2022)
Review
Oncology
Fatma Dogan, Nicholas R. Forsyth
Summary: This article provides an overview of the epigenetic mechanisms involved in the regulation of TERT expression and telomerase activity, with a focus on their potential role in cancer treatment.