Article
Genetics & Heredity
Farideh Moharrek, Lars R. Ingerslev, Ali Altintas, Leonidas Lundell, Ann N. Hansen, Lewin Small, Christopher T. Workman, Romain Barres
Summary: This study compared DNA methylation in spermatozoa from humans, mice, rats, and mini-pigs and found DNA methylation variation near genes related to the central nervous system and signal transduction. Additionally, gene expression dynamics during different preimplantation stages were modestly associated with spermatozoal DNA methylation at the nearest promoters.
Review
Cell Biology
Mark Tomas Mc Auley
Summary: Ageing is a biological process characterized by physical decline and increased risk of mortality over time, with recent evidence linking epigenetic mechanisms like DNA methylation to age-related diseases. Evolutionary theory provides insights into how genes impact fitness at different ages, and how DNA methylation changes are associated with age onset pathology.
AGEING RESEARCH REVIEWS
(2021)
Review
Biochemistry & Molecular Biology
Irina V. Bure, Marina V. Nemtsova
Summary: Despite recent progress, gastric cancer remains a common and deadly cancer with aberrant DNA methylation and deregulation of noncoding RNA expression playing a significant role in tumorigenesis. Interactions among these epigenetic regulators form a complex network that has potential implications for diagnosis, prognosis, and treatment of gastric cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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)
Editorial Material
Genetics & Heredity
Moshe Szyf
Summary: Professor Moshe Szyf is an authority in the field of social epigenetics and has made important research contributions, including identifying DNA methylation as a therapeutic target and studying the impact of social environment on DNA methylation. He is also the founder and leader of multiple institutions and projects.
Article
Biotechnology & Applied Microbiology
Adam Nunn, Christian Otto, Mario Fasold, Peter F. Stadler, David Langenberger
Summary: This study presents a computational pre-processing approach to enable downstream analysis on a per-strand basis using conventional variant calling software. The method improves precision and sensitivity compared to specialized tools, and is applicable to both human and model plant variants.
Review
Plant Sciences
Athanasios Dalakouras, Dimitrios Vlachostergios
Summary: Modern agriculture is urgently seeking solutions to address the adverse effects of global climate change, reduced farmland, and increasing world population needs. Utilizing epigenetics as a source of variation in crop breeding shows potential as an alternative method. Current advancements and limitations in epigenetics-mediated crop breeding are discussed, with proposed novel RNA-based strategies for gene-specific and transgene-free modification of the epigenome.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemical Research Methods
Pegah Mavaie, Lawrence Holder, Daniel Beck, Michael K. Skinner
Summary: This study introduced a hybrid DL-ML approach to predict environmentally responsive transgenerational differential DNA methylated regions using deep neural network for feature extraction and a non-DL classifier. The experimental results showed that this approach outperforms traditional deep learning and machine learning methods.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Joan Sabria-Back, Ana Monteagudo-Sanchez, Marta Sanchez-Delgado, Anne C. Ferguson-Smith, Olga Gomez, Africa Pertierra Cartada, Jair Tenorio, Julian Nevado, Pablo Lapunzina, Arrate Pereda Aguirre, Carles Gimenez Sevilla, Estefania Toro Toro, Guiomar Perez de Nanclares, David Monk
Summary: Kagami-Ogata syndrome (KOS14) and Temple syndrome (TS14) are associated with reciprocal alterations within the chr14q32 imprinted domain. A work-up strategy for preimplantation genetic testing (PGT) was presented to avoid the transmission of a causative micro-deletion. PGT was successfully offered to identify an unaffected embryo and transfer it, resulting in the birth of a healthy baby.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Biology
Manon Fallet, Rachel Wilson, Peter Sarkies
Summary: The study reveals that cisplatin exposure has limited effects on small non-coding RNA epimutations and gene expression levels in Caenorhabditis elegans, but leads to increased fluctuations in tRNA-derived small RNAs. These changes may be associated with gene expression alterations induced by genotoxic stress.
Article
Biochemistry & Molecular Biology
Christopher G. Fenton, Mithlesh Kumar Ray, Wei Meng, Ruth H. Paulssen
Summary: Long non-coding RNAs (lncRNAs) have been found to be involved in the development of ulcerative colitis (UC), and their interplay with DNA methylation and the role of environmental factors in disease development remain to be fully explored. This study analyzed mucosal biopsies from UC patients and normal controls to identify UC-associated lncRNAs regulated by differentially methylated regions (DMRs). The study also identified genes involved in inflammatory immune responses downstream of DMR-regulated lncRNAs. Understanding the interplay between lncRNA expression and DNA methylation in UC could enhance our knowledge of its pathogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Veronika N. Laine, Bernice Sepers, Melanie Lindner, Fleur Gawehns, Suvi Ruuskanen, Kees van Oers
Summary: The field of molecular biology is rapidly advancing and there is a growing interest in studying ecological epigenetics, particularly in wild vertebrates. This review provides a practical guide for researchers studying DNA methylation variation in wild vertebrates, discussing technical aspects, limitations, and data analysis methods.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Biochemistry & Molecular Biology
Feng-Chih Kuo, Chia-Ter Chao, Shih-Hua Lin
Summary: Chronic kidney disease (CKD) is characterized by a gradual decline in glomerular filtration rate, resulting in adverse consequences such as fluid retention, electrolyte imbalance, and increased cardiovascular risk. Diabetes mellitus is a major contributor to the development of CKD, particularly diabetic kidney disease (DKD), which is influenced by epigenetic dysregulation triggered by metabolic disturbances, oxidative stress, and inflammation. This review provides an overview of the major epigenetic molecular mechanisms and summarizes current knowledge about epigenetic alterations in DKD. It highlights the importance of epigenetic regulation in various renal cell types and explores potential epigenetic biomarkers and therapeutic agents for early detection and management of DKD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Shihang Zhou, Hongliang Zeng, Jinhua Huang, Li Lei, Xiaoliang Tong, Si Li, Ying Zhou, Haoran Guo, Manal Khan, Liping Luo, Rong Xiao, Jing Chen, Qinghai Zeng
Summary: Melanogenesis is a complex process involving multiple genes and signaling pathways, with epigenetics playing a key role in regulating the expression of key genes. Epigenetic-based therapy provides novel opportunities for treating dermatoses caused by pigmentation disturbances.
AGEING RESEARCH REVIEWS
(2021)
Article
Biology
Anabelle Planques, Pierre Kerner, Laure Ferry, Christoph Grunau, Eve Gazave, Michel Vervoort
Summary: High levels of 5mC methylation were found in the annelid P. dumerilii, indicating that this feature is not specific to vertebrates in the bilaterian clade. The dynamic nature of 5mC methylation levels in P. dumerilii throughout its life cycle suggests a potential role in development and regeneration processes.
Article
Parasitology
Peter J. Taylor, Jana Hagen, Farid N. Faruqu, Khuloud T. Al-Jamal, Bonnie Quigley, Morgan Beeby, Murray E. Selkirk, Peter Sarkies
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2020)
Article
Genetics & Heredity
Samuel H. Lewis, Laura Ross, Stevie A. Bain, Eleni Pahita, Steven A. Smith, Richard Cordaux, Eric A. Miska, Boris Lenhard, Francis M. Jiggins, Peter Sarkies
Article
Ecology
Toni Beltran, Vahid Shahrezaei, Vaishali Katju, Peter Sarkies
NATURE ECOLOGY & EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Toni Beltran, Elena Pahita, Subhanita Ghosh, Boris Lenhard, Peter Sarkies
Summary: This study reveals the role of the Integrator complex in transcription termination at piRNA loci, demonstrating its mechanism of terminating transcription by cleaving capped piRNA precursors. However, loss of Integrator activity does not result in transcriptional readthrough at the majority of piRNA loci.
Article
Microbiology
Jana Hagen, Peter Sarkies, Murray E. Selkirk
Summary: The use of a pseudotyped viral vector has successfully enabled genetic manipulation of parasitic nematodes, including gene silencing and expression of exogenous genes. This method holds promise for advancing research on the complex biology of nematode parasites and identifying new targets for infection control.
Article
Biochemistry & Molecular Biology
Lisa Schneider, Yi-Ke Guo, David Birch, Peter Sarkies
Summary: Transposable elements (TEs) are widespread in eukaryotic genomes, with their diversity shaped by complex genetic and epigenetic mechanisms. Tracking TE evolution through network analysis can reveal previously unknown properties of TE evolution across species.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Peter Sarkies
Summary: DNA methylation is an ancient epigenetic pathway found across eukaryotes, with rapidly evolving targets within genomes. The mealybug Planococcus citri has evolved methylation similar to mammals, impacting gene expression and sexual dimorphism in the species. This study highlights the complex relationship between DNA methylation and gene expression, demonstrating the rapid evolution of different methylation systems.
Review
Biochemistry & Molecular Biology
Peter Sarkies
Summary: DNA methylation is an epigenetic modification that has undergone long-term evolutionary changes. However, it evolves surprisingly rapidly in eukaryotes. The genomic distribution of methylation diversifies quickly in different lineages, and DNA methylation is frequently lost altogether. Recent studies using genomic and epigenomic sequencing have shed light on the reasons behind the rapid evolution of both the DNA methylation machinery and its genome-wide distribution. New discoveries about the fitness costs associated with DNA methylation, as well as new theories about the biochemical mechanisms that introduce and maintain DNA methylation, have helped explain how new patterns of methylation emerge.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Dongying Xie, Pohao Ye, Yiming Ma, Yongbin Li, Xiao Liu, Peter Sarkies, Zhongying Zhao
Summary: Different modes of reproduction have significant impact on genome composition. This study investigates the gene regulation in hybrid embryos resulting from crosses between Caenorhabditis briggsae and its outcrossing sister species Caenorhabditis nigoni. The results show that gene regulation plays a crucial role during hybridization, and the regulation of C. nigoni genome is more stable compared to C. briggsae. These findings provide insights into how selfing species maintain genomic identity despite genetic exchanges with closely related outcrossing species.
Article
Genetics & Heredity
Rachel A. Wilson, Maxime E. Le Bourgeois, Marcos A. Perez, Peter E. Sarkies
Summary: Recently, it has been discovered that there is information beyond the DNA sequence, known as epigenetic information, that can be transmitted between generations and control how the DNA sequence is used. We investigated the contribution of different types of epigenetic information to evolution using nematode worms. Most epigenetic differences were short-lived, but we identified some changes that lasted longer, particularly in genes related to the worms' responses to external threats.
Editorial Material
Biochemistry & Molecular Biology
Peter Sarkies
Summary: Cells from most eukaryotic species produce various types of small interfering RNAs. Pioneering research in plants, published in PLOS Biology nearly 20 years ago, established a framework for understanding how multiple RNA interference pathways can simultaneously regulate the genome.
Article
Biochemistry & Molecular Biology
Marcos Francisco Perez, Peter Sarkies
Summary: This study explores the impact of histone methylation on metabolism and reveals a correlation between histone methyltransferases and metabolism. In cancer, the expression of histone methyltransferases is inversely related to the activity of NNMT, while in healthy tissues, histone methylation is inversely correlated to the levels of PEMT. These associations affect multiple histone marks on chromatin genome-wide but have no detectable impact on transcriptional regulation. Furthermore, the study also finds co-regulation of histone methyltransferases by the Retinoblastoma tumor suppressor.
Article
Biology
Alice Brown, Murray E. Selkirk, Peter Sarkies
Summary: This study investigated the secretion mechanism and stability of miRNAs in the parasitic nematode Trichinella spiralis. Proteomics analysis identified two RNA binding proteins secreted by T. spiralis larvae. One of these proteins showed selective and sequence-specific binding to miRNA, while the other protein exhibited non-specific binding. These findings provide insights into the possible mechanism of miRNA secretion in T. spiralis and contribute to our understanding of extracellular miRNA biology.
Article
Biology
Manon Fallet, Rachel Wilson, Peter Sarkies
Summary: The study reveals that cisplatin exposure has limited effects on small non-coding RNA epimutations and gene expression levels in Caenorhabditis elegans, but leads to increased fluctuations in tRNA-derived small RNAs. These changes may be associated with gene expression alterations induced by genotoxic stress.
Article
Biology
Ulfar Bergthorsson, Caroline J. Sheeba, Anke Konrad, Tony Belicard, Toni Beltran, Vaishali Katju, Peter Sarkies
Review
Cell Biology
Alyssa Kearly, Andrew D. L. Nelson, Aleksandra Skirycz, Monika Chodasiewicz
Summary: Stress Granules (SGs) and Processing-bodies (P-bodies) are important biomolecular condensates that play crucial roles in maintaining mRNA balance and regulating stress responses. They are composed of proteins and RNAs involved in translation, protein folding, and energy metabolism.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
P. Lemonnier, T. Lawson
Summary: Stomatal conductance plays a crucial role in determining CO2 uptake and water loss in plants, affecting overall water status and productivity. However, the signals coordinating mesophyll demands for CO2, the role of chloroplasts in stomatal function, and other GC metabolic processes in stomatal function remain poorly understood.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Matteo Gionfriddo, Timothy Rhodes, Spencer M. Whitney
Summary: Rubisco is a key enzyme that facilitates the entry of CO2 into the biosphere, but its catalytic properties are slow and error-prone. More effective Rubisco variants have been discovered in certain algae, offering the potential to significantly improve crop productivity. However, incompatibilities in protein folding have hindered the transplantation of these variants into plants. Directed evolution is now being explored to enhance Rubisco catalysis.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Vittoria Clapero, Stephanie Arrivault, Mark Stitt
Summary: The Calvin-Benson cycle has undergone massive selection and co-evolution with carbon-concentrating mechanisms due to changing environmental factors. Metabolite profiling reveals species-specific variations in the operation of the cycle, indicating the influence of different modes of photosynthesis. Connectivity analysis identifies constraints and driving factors for cross-species diversity in the cycle.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Sukhbir Kaur, David D. Roberts
Summary: Thrombospondin-1 modulates cell behavior by interacting with components of the extracellular matrix and cell surface receptors. Its release and expression are influenced by injuries and various diseases, while its sustained presence in the extracellular space is regulated by receptor-mediated clearance. Thrombospondin-1 plays important roles in immune responses.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Richard P. Tucker, Josephine C. Adams
Summary: Thrombospondins (TSPs) play diverse roles in animals and have been found to belong to a superfamily that includes different subgroups such as mega-TSPs, sushi-TSPs, and poriferan-TSPs. Invertebrates encode a greater diversity of TSP superfamily members than vertebrates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
James Petrik, Sylvia Lauks, Bianca Garlisi, Jack Lawler
Summary: Many cancers start with a small nest of transformed cells that can remain dormant. Thrombospondin-1 (TSP-1) initially promotes dormancy by suppressing angiogenesis, but over time, factors promoting angiogenesis become dominant and recruit various cells to form a complex tumor microenvironment. TSPs play a role in the proliferation, migration, and invasion of cells in the tumor microenvironment, as well as influencing the immune characteristics and phenotype of tumor-associated macrophages.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hana Fakim, Christine Vande Velde
Summary: There has been increasing attention to the role of phase-separated biomolecular condensates, specifically stress granules, in neurodegenerative diseases like ALS. ALS-associated mutations in genes involved in stress granule assembly have been found, and stress granule proteins have been detected in pathological inclusions in ALS patient neurons. However, protein components of stress granules are also present in other physiological biomolecular condensates, which have not been adequately discussed in relation to ALS. This review explores the functions of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites beyond stress granules, and discusses the impact of ALS-linked mutations on their ability to phase separate and perform their functions in stress-independent biomolecular condensates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Alexander Lin, Yogambha Ramaswamy, Ashish Misra
Summary: Smooth muscle cells, endothelial cells, and macrophages in blood vessels display remarkable heterogeneity, and their developmental origins may influence their plasticity. Unbiased single cell whole transcriptome analysis techniques are revolutionizing the understanding of cellular diversity and plasticity, providing insights for therapeutic research.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Elton P. Hudson
Summary: The Calvin Benson cycle plays a crucial role in the ecological and biotechnological aspects of bacteria. Recent studies have shed light on the regulation of this cycle in bacteria, with post-transcriptional and post-translational regulation being important in phototrophic bacteria, and transcriptional regulation being prominent in chemolithoautotrophic bacteria. Understanding the regulation of the Calvin Benson cycle has implications for enhancing CO2 fixation and improving the synthesis of desired products. Non-canonical cycles may offer potential benefits for industrial applications.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Xin-Guang Zhu, Haim Treves, Honglong Zhao
Summary: This paper discusses the major regulatory mechanisms over the Calvin Benson Cycle (CBC) that maintain homeostasis of metabolite levels. These mechanisms include redox regulation of enzymes, metabolite regulations (especially allosteric regulations), and balanced activities of enzymes. These regulatory mechanisms are crucial for maintaining high flux and photosynthetic efficiency in CBC.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hunter C. Herriage, Yi-Ting Huang, Brian R. Calvi
Summary: Apoptosis prevents the inappropriate acquisition of extra copies of the genome, known as polyploidy, but the polyploid state can suppress apoptosis. The mechanisms linking apoptosis and polyploid cell cycles are still largely unknown, and studying the regulation of apoptosis in development and cancer could lead to more effective therapies.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Daniel Campbell, Steven Zuryn
Summary: Mitochondrial dynamics play a crucial role in regulating cellular and organismal homeostasis, impacting various aspects of an organism's healthspan. By studying the nematode Caenorhabditis elegans, a comprehensive understanding of the impact of mitochondrial dynamics on homeostasis over a lifetime can be obtained.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Diba Borgmann, Henning Fenselau
Summary: Maintaining blood glucose at an appropriate physiological level requires coordination of multiple organs and tissues, with the vagus nerve playing a key role in central control. Recent studies have revealed the cellular identity, neuroanatomical organization, and functional contributions of vagal neurons in the regulation of systemic glucose metabolism. These findings provide new insights into the precise roles of vagal neurons in coordinating glucose levels and offer potential avenues for treating glucose metabolism disorders.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Tatiana C. Coverdell, Stephen B. G. Abbott, John N. Campbell
Summary: In this article, we review how genetic technology and single-cell genomics are revealing the organizational principles of the efferent vagus in unprecedented detail.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
