Review
Biology
Natalya Frolows, Alyson Ashe
Summary: In recent years, research has shown that in addition to the information encoded in DNA sequences, molecules within the cytoplasm of the gamete play a significant role in heritability. RNA molecules are crucial in transmitting transgenerational responses, while the role of histone modifications in epigenetic inheritance is increasingly recognized.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Piergiuseppe Quarato, Meetali Singh, Loan Bourdon, Germano Cecere
Summary: Heritable traits are primarily encoded within genomic DNA, but epigenetic information can also be inherited through DNA methylation, histone modifications, and small RNAs. Small RNAs play a significant role in transmitting epigenetic information across generations, specifically through the transfer from germline to embryos. Inherited epigenetic information can be maintained across generations in a small RNA-dependent and independent manner, and epigenetic traits acquired from the soma can be inherited through small RNAs.
Review
Genetics & Heredity
Jana Svorcova
Summary: In recent years, increasing evidence suggests the non-genetic heredity of the effects of separation from parents, life-threatening events, and other traumatising experiences. This heredity is mediated by epigenetic regulations and can be transmitted over generations. The reviewed studies on transgenerational epigenetic inheritance (TEI) and intergenerational studies on trauma or stressful experiences reveal universal changes initiated by stress exposure at various levels of organization. Understanding these processes can help elucidate the evolutionary pathways of diseases and disorders associated with trauma exposure.
Review
Biochemistry & Molecular Biology
Germano Cecere
Summary: While genetic information was traditionally thought to be transmitted primarily through the genome, recent research has shown the presence of epigenetic inheritance in animals. Small RNAs play a crucial role in transmitting epigenetic information across generations in animals, influencing complex traits such as fertility, stress responses, infections, and behavior. The understanding of the molecular pathways and mechanisms responsible for epigenetic inheritance in animals is undergoing a radical shift due to the discovery of small RNAs as epigenetic molecules capable of transmitting traits across generations.
Review
Biochemistry & Molecular Biology
Nguyen Hoai Nguyen, Nam Tuan Vu, Jong-Joo Cheong
Summary: Plants respond to drought stress by producing abscisic acid, which regulates gene expression and helps plants tolerate stress. The surrounding chromatin architecture undergoes epigenetic remodeling to trigger or suppress gene transcription under drought conditions. Plants can remember chromatin status and transmit drought tolerance to the next generation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Endocrinology & Metabolism
Nicole Mohajer, Erika M. Joloya, Jeongbin Seo, Toshi Shioda, Bruce Blumberg
Summary: Obesity and metabolic disorders are global pandemics, potentially linked to exposure to endocrine disrupting chemicals known as obesogens. Transgenerational inheritance of phenotypic traits and diseases, such as obesity, may be mediated by epigenetic mechanisms, highlighting the complexity of inherited susceptibility to environmental exposures.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Qifan Zhu, Jane Allyn Kirby, Chen Chu, Lan-Tao Gou
Summary: Infertility is a common reproductive issue affecting one in six couples worldwide, with a significant number of cases remaining undiagnosed. Small noncoding RNAs play crucial roles in mammalian reproduction, particularly in sperm, and are increasingly seen as potential biomarkers for fertility and embryo quality.
Review
Food Science & Technology
Shuai Han, Yi Luo, Bo Liu, Tianyi Guo, Dandan Qin, Feijun Luo
Summary: Epigenetics plays a crucial role in exploring the etiology and treatment of diabetes, and reversing epigenetic alterations may reduce the burden of the disease. Dietary flavonoids as natural epigenetic modulators can serve as biomarkers for diabetes prevention and the development of alternative therapies. Further research is needed to explore the potential anti-diabetic effects of different flavonoids with various epigenetic regulation mechanisms through clinical trials.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Plant Sciences
Narendra Singh Yadav, Viktor Titov, Ivie Ayemere, Boseon Byeon, Yaroslav Ilnytskyy, Igor Kovalchuk
Summary: Plants can adapt to environmental stress not only through physiological changes but also through genetic and epigenetic alterations. The study on multigenerational heat stress in Arabidopsis thaliana revealed that the stressed progeny exhibited higher heat tolerance, genetic mutations, and epigenetic changes, highlighting the importance of adaptation mechanisms over generations.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Richa Pant, Priyanka Firmal, Vibhuti Kumar Shah, Aftab Alam, Samit Chattopadhyay
Summary: Obesity is a major public health concern characterized by an increase in adipose tissue mass, which can lead to impaired metabolic health and even influence cancer progression. Dysfunction in adipocyte function is influenced by genetics and environmental factors, affecting gene expression and onset of obesity. Understanding the complexities of adipogenesis is crucial for recognizing disease conditions and identifying therapeutic interventions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Environmental Sciences
Louis Legoff, Shereen Cynthia D'Cruz, Morgane Lebosq, Aurore Gely-Pernot, Katia Bouchekhchoukha, Christine Monfort, Pierre-Yves Kernanec, Sergei Tevosian, Luc Multigner, Fatima Smagulova
Summary: The study investigated the transgenerational effects of chlordecone on murine prostate tissue. Results showed the presence of prostatic intraepithelial neoplasia in male offspring exposed to CD, with differential gene expressions in prostates of different generations linked to tumor-related biological processes. CD exposure led to increased expression of Hox genes in the prostate, significant upregulation of genes involved in testosterone synthesis, and epigenetic changes.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Biology
Suresh Kumar, Karishma Seem, Trilochan Mohapatra
Summary: Plants need to modulate their responses to drought stress in order to protect themselves. In this investigation, rice plants were subjected to drought stress and the effects were observed in subsequent generations. These findings are important for developing stress-tolerant crops and ensuring global food security.
Review
Biochemistry & Molecular Biology
Meenu Ghai, Farzeen Kader
Summary: Epigenetics aims to regulate DNA inheritance, with studies showing transgenerational inheritance in animal models but controversial evidence in humans. Male and female germline development in humans follow separate paths of epigenetic events, with oocytes and sperm possessing unique epigenomes. While DNA methylation alterations are reset during reprogramming, non-coding RNAs in human sperm are reliable carriers for transgenerational inheritance.
BIOCHEMICAL GENETICS
(2022)
Article
Reproductive Biology
Xin-Yuan Li, Jie-Xue Pan, Hong Zhu, Guo-Lian Ding, He-Feng Huang
Summary: In recent years, there has been an increasing recognition of the developmental origins of diseases. It is suggested that many chronic diseases in adulthood, including diabetes, obesity, cardiovascular disease, and tumors, may develop early on. Germ cells play a crucial role in inheritance, and external influences during their differentiation and development can lead to damage and increase the risk of chronic disease development. This article further explores the concept of gamete and embryo origins of adult diseases, focusing on environmental insults on germ cells.
BIOLOGY OF REPRODUCTION
(2022)
Review
Geriatrics & Gerontology
Mark T. Mc Auley
Summary: In the last decade, epigenetics has become a central discipline in the field of biogerontology, as age-associated epigenetic changes are linked to various pathologies and epigenetic clocks can correlate biological age with chronological age. Recent empirical observations also suggest that inherited epigenetic effects could influence lifespan/longevity in different organisms. This review critically evaluates these effects from an evolutionary perspective, aiming to integrate the evidence with the main evolutionary theories of ageing.
EXPERIMENTAL GERONTOLOGY
(2023)
Article
Plant Sciences
Julie Ferreira de Carvalho, Solenn Stoeckel, Frederique Eber, Maryse Lode-Taburel, Marie-Madeleine Gilet, Gwenn Trotoux, Jerome Morice, Cyril Falentin, Anne-Marie Chevre, Mathieu Rousseau-Gueutin
Summary: Recurrent selection of euploid plants for eight generations significantly reduced the percentage of aneuploid progenies and the number of newly fixed homoeologous rearrangements, promoting genome stability. The effects of homoeologous rearrangements on meiotic behavior and seed number depended strongly on the genetic background and cytoplasm donor.
Article
Multidisciplinary Sciences
Laura Entrambasaguas, Miriam Ruocco, Koen J. F. Verhoeven, Gabriele Procaccini, Lazaro Marin-Guirao
Summary: This study explores the relationship between gene body DNA methylation and gene expression patterns in two marine plants, suggesting that genes with low DNA methylation levels exhibit greater flexibility and plasticity in expression. Additionally, the empirical determination of global DNA methylation patterns indicates a relationship between methylation levels and the plants' origin latitude and life history.
SCIENTIFIC REPORTS
(2021)
Article
Ecology
Kimberley D. Lemmen, Koen J. F. Verhoeven, Steven A. J. Declerck
Summary: The study found that even in the absence of initial genetic diversity and recombination, small populations can rapidly exhibit adaptive genetic changes, indicating that de novo genetic variation or alternative sources of phenotypic variation may help in the establishment and persistence of low-diversity populations.
FUNCTIONAL ECOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Fleur Gawehns, Maarten Postuma, Morgane van Antro, Adam Nunn, Bernice Sepers, Samar Fatma, Thomas P. van Gurp, Niels C. A. M. Wagemaker, A. Christa Mateman, Slavica Milanovic-Ivanovic, Ivo Grosse, Kees van Oers, Philippine Vergeer, Koen J. F. Verhoeven
Summary: In this study, a new laboratory protocol and bioinformatics pipeline were developed for cytosine methylation analysis in nonmodel species. The method is cost- and time-efficient, user-friendly, and has been shown to perform well based on evaluation against baseline data sets.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
Franz Boideau, Gautier Richard, Olivier Coriton, Virginie Huteau, Caroline Belser, Gwenaelle Deniot, Frederique Eber, Cyril Falentin, Julie Ferreira de Carvalho, Marie Gilet, Maryse Lode-Taburel, Loeiz Maillet, Jerome Morice, Gwenn Trotoux, Jean-Marc Aury, Anne-Marie Chevre, Mathieu Rousseau-Gueutin
Summary: Meiotic recombination is an important evolutionary process in sexual organisms that generates genetic diversity. This process is tightly regulated, with most crossovers occurring in chromosomal regions with low DNA methylation levels. However, there are still islands without recombination in these regions, which can be caused by DNA methylation or structural variations.
Article
Genetics & Heredity
Nelia Luviano, Marie Lopez, Fleur Gawehns, Cristian Chaparro, Paola B. Arimondo, Slavica Ivanovic, Patrice David, Koen Verhoeven, Celine Cosseau, Christoph Grunau
Summary: The study introduces a new DNA methyltransferase inhibitor, Flv1, to induce random changes in 5mC levels in certain mollusk species, showing significant reduction in 5mC levels and resulting in variability in the methylome, thereby affecting phenotypic traits and demonstrating multi-generational effects.
EPIGENETICS & CHROMATIN
(2021)
Article
Agriculture, Multidisciplinary
Anani Amegan Missinou, Julie Ferreira de Carvalho, Nathalie Marnet, Thomas Delhaye, Oumayma Hamzaoui, David Abdel Sayed, Yann Guitton, Lionel Lebreton, Christophe Langrume, Anne Laperche, Regine Delourme, Maria J. Manzanares-Dauleux, Alain Bouchereau, Antoine Gravot
Summary: This study investigates the chemical diversity in 281 accessions of Brassica napus and identifies numerous rarely reported phenolics and glucosinolates. The study also reveals significant variations in the content of certain compounds among different accessions and identifies two main chemotypes associated with specific compound contents. The findings of this study provide a valuable resource for understanding the phytochemical diversity in B. napus.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Ecology
Jeannie M. Mounger, Isolde van Riemsdijk, M. Teresa Boquete, Cornelis A. M. Wagemaker, Samar Fatma, Marta H. Robertson, Sandy A. Voors, Jenna Oberstaller, Fleur Gawehns, Torrance C. Hanley, Ivo Grosse, Koen J. F. Verhoeven, Erik E. Sotka, Catherine A. Gehring, A. Randall Hughes, David B. Lewis, Marc W. Schmid, Christina L. Richards
Summary: By analyzing genetic and epigenetic variation in natural populations of Spartina alterniflora, researchers found that both source population and habitat played a role in explaining genetic and epigenetic diversity, and that DNA methylation distinctly contributed to plant responses in natural populations.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Anne Aagaard, Shenglin Liu, Tom Tregenza, Marie Braad Lund, Andreas Schramm, Koen J. F. Verhoeven, Jesper Bechsgaard, Trine Bilde
Summary: Understanding the role of genetic and nongenetic variants in shaping phenotypic responses to local environments is crucial for our understanding of evolutionary potential. By conducting environmental association studies, we found strong associations between genetic and nongenetic variation and environmental factors. Genetic variants were strongly correlated with average temperature, while DNA methylation variation was correlated with multiple climate parameters. Microbiome composition was mainly associated with precipitation-related climatic factors.
Article
Biochemistry & Molecular Biology
Morgane Van Antro, Stella Prelovsek, Slavica Ivanovic, Fleur Gawehns, Niels C. A. M. Wagemaker, Mohamed Mysara, Nele Horemans, Philippine Vergeer, Koen J. F. Verhoeven
Summary: Environmentally induced DNA methylation variants can persist over multiple generations in plants, potentially affecting gene expression and phenotypes.
Article
Ecology
Bridgett M. M. von Holdt, Rebecca Y. Y. Kartzinel, Kees van Oers, Koen J. F. Verhoeven, Jenny Q. Q. Ouyang
Summary: This study examines the contribution of DNA methylation to early-life phenotypic variation. The research finds higher methylation frequencies in urban house wren offspring at hatching and observes age-related patterns in offspring methylation. Additionally, differential methylation analyses show that cellular respiration genes and behavioral/metabolism genes are differentially methylated in broods of different origins and rearing environments, respectively. Lastly, hyper-methylation of a single gene (CNTNAP2) is associated with decreased glucocorticoid levels and the rearing environment. These findings suggest that DNA methylation may play a role in individuals' adjustment to novel environments during their lifespan.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Article
Agronomy
Paola Rallo, S. Emilia Hannula, Freddy C. ten Hooven, Koen J. F. Verhoeven, Jan Kammenga, Wim H. van der Putten
Summary: This study investigates plant-soil feedbacks (PSFs) between and within grass species. The results show differences in PSF effects between grass species, but limited variation within species. Additionally, potential microbial candidates that drive the observed PSF effects are identified.
Article
Microbiology
Olaf Tyc, Purva Kulkarni, Adam Ossowicki, Vittorio Tracanna, Marnix H. Medema, Peter van Baarlen, W. F. J. van IJcken, Koen J. F. Verhoeven, Paolina Garbeva
Summary: Microbial community analysis has shown that bacteria with cell sizes of about 0.1 μm are an important component of aquatic environments, but it is unknown if they exist in terrestrial environments like soil. In this study, we isolated soil bacteria that passed through a 0.1 μm filter and identified one isolate as Hylemonella gracilis. Coculture assays demonstrated that H. gracilis grows better when interacting with other soil bacteria, and transcriptomics and metabolomics revealed that H. gracilis can induce gene expression, behavior, and biochemistry changes in other bacteria without direct contact. Our findings suggest the presence of small bacteria in soil that can pass through 0.1 μm filters and contribute to the symbiosis of soil bacterial communities.
Article
Ecology
Veronica Noe Ibanez, Morgane van Antro, Cristian Pena-Ponton, Slavica Milanovic-Ivanovic, Cornelis A. M. Wagemaker, Fleur Gawehns, Koen J. F. Verhoeven
Summary: DNA methylation in plant genomes can provide genealogical information at short time scales, but its reliability at micro-evolutionary time scales is unclear due to meta-stability and environmental effects. In a study of common dandelion, differentially methylated cytosines (DMCs) were induced by light treatment, with genetic divergence between accessions correlating strongly with overall methylation profiles. However, environmental effects may partly dilute the genealogical signal in CG context. Methylation information can be used to reconstruct micro-evolutionary genealogy in plants lacking genetic variation.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bernice Sepers, Rebecca Shuhua Chen, Michelle Memelink, Koen J. F. Verhoeven, Kees van Oers
Summary: As environmental fluctuations become more frequent, organisms need to adapt quickly to changes caused by humans, climate, and ecology. Epigenetic modifications, specifically DNA methylation, play a role in shaping a organism's phenotypic responses during development. While studies have shown that environmentally induced DNA methylation changes occur, we have limited understanding of the proportion of the epigenome affected by environmental factors compared to genetic variation. In this study, using a partial cross-foster design in a great tit population, we found that common origin explained the variance in DNA methylation in 8,315 CpG sites while common rearing environment only explained 101 sites. Furthermore, we identified quantitative trait loci for the CpG sites related to brood origin, with 754 cis and 4,202 trans methylation quantitative trait loci involving 24% of the CpG sites. These findings suggest that the influence of environmentally induced methylation marks, independent of genotype, is limited and that genetic factors play a larger role in determining DNA methylation variation early in life.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
