Review
Cell Biology
Arianna Mangiavacchi, Gabriele Morelli, Valerio Orlando
Summary: Non-coding DNA makes up about 98.5% of the human genome and has been re-evaluated to reveal its importance in cell regulation through the presence of non-coding RNAs (ncRNAs). This review focuses on the relationship between chromatin-interacting RNAs, such as long non-coding RNA (lncRNA), enhancer RNA (eRNA), non-coding natural antisense transcript (ncNAT), circular RNA (circRNA), and the epigenome, highlighting their role in regulating gene expression and their impact on human diseases, particularly cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Review
Cell Biology
Courtney W. Hanna, Gavin Kelsey
Summary: Genomic imprinting refers to the monoallelic expression of a gene based on parent of origin, which is a result of differential epigenetic marking between male and female germlines. Apart from the canonical DNA methylation-mediated imprinting, there is also non-canonical imprinting caused by maternal H3K27me3-independent of DNA methylation. Conservation of canonical and noncanonical genomic imprinting and the role of endogenous retroviral elements are discussed in this review.
GENES & DEVELOPMENT
(2021)
Review
Cell Biology
Hisato Kobayashi
Summary: Genomic imprinting is an epigenetic phenomenon that leads to unequal expression of homologous maternal and paternal alleles in the mouse genome. More than 260 imprinted genes have been identified, most of which are controlled by imprinted germline differentially methylated regions, while a subset of genes are controlled by maternal-derived histone modifications. Understanding DNA methylation-dependent and -independent imprints may provide new insights into genetic regulation and evolutionary divergence.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Hisato Kobayashi
Summary: Genomic imprinting is an epigenetic phenomenon that results in unequal expression of homologous maternal and paternal alleles. This process can maintain parental epigenetic memories following fertilization and induce allele-specific transcription and chromatin modifications of neighboring genes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Philip Vlummens, Stefaan Verhulst, Kim De Veirman, Anke Maes, Eline Menu, Jerome Moreaux, Hugues De Boussac, Nicolas Robert, Elke De Bruyne, Dirk Hose, Fritz Offner, Karin Vanderkerken, Ken Maes
Summary: In this study, bio-informatic tools were used to identify novel targets associated with high-risk myeloma. Protein arginine methyltransferase 5 (PRMT5) was identified as a promising target. The PRMT5 inhibitor EPZ015938 effectively reduced the growth of myeloma cells and induced apoptosis. PRMT5 was found to be involved in regulating alternative splicing, DNA repair, and PI3K/mTOR signaling, and was associated with important genes in MM disease. These findings suggest that PRMT5 could be a potential therapeutic target for myeloma.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Oncology
Giovanni Blandino, Roberto Dinami, Marco Marcia, Eleni Anastasiadou, Brid M. Ryan, Alina Catalina Palcau, Luigi Fattore, Giulia Regazzo, Rosanna Sestito, Rossella Loria, Ana Belen Diaz Mendez, Maria Chiara Cappelletto, Claudio Pulito, Laura Monteonofrio, George A. Calin, Gabriella Sozzi, Jit Kong Cheong, Ranit Aharonov, Gennaro Ciliberto
Summary: The 5th Workshop IRE on Translational Oncology was held in Rome (Italy) to discuss the significant progress made in the RNA field, focusing on diagnostic biomarkers and targeted therapies. Non-coding RNAs were highlighted for their potential in cancer diagnosis and therapy. The report collected presentations from scientists discussing recent oncology research and providing examples of RNA applications as biomarkers and therapeutics.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Review
Oncology
Tristan Joseph Verhoeff, Adele F. Holloway, Joanne L. Dickinson
Summary: This article explores the regulation of integrin genes by non-coding RNAs and how these discoveries are informing the development of cancer therapeutics. MiRNAs have been extensively studied and are found to negatively regulate most integrin genes by binding to recognition sequences in the mRNA 3' untranslated regions. The mechanisms of lncRNAs are more complex and varied, potentially counteracting miRNAs, directly affecting integrin mRNA transcription, or influencing transcription factors and epigenetic machinery. Integrins as therapeutic targets are of great interest and therapeutics mimicking ncRNA mechanisms are already being tested.
Editorial Material
Plant Sciences
Sebastian Marquardt, Pablo Andres Manavella
Summary: The functions of RNAs in plant biology have been extensively studied using advanced sequencing technologies, leading to significant progress in our understanding of cellular roles of RNAs and also raising new questions.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Genetics & Heredity
Ken Higashimoto, Hijiri Watanabe, Yuka Tanoue, Hidefumi Tonoki, Tomoharu Tokutomi, Satoshi Hara, Hitomi Yatsuki, Hidenobu Soejima
Summary: Silver-Russell syndrome (SRS) is a representative imprinting disorder characterized by ICR1-LOM, with analysis showing variations in methylation patterns among different patients, emphasizing the importance of simultaneous analysis of multiple methylation sites for accurate molecular diagnosis.
JOURNAL OF MEDICAL GENETICS
(2021)
Article
Genetics & Heredity
David Kenny, Roy D. Sleator, Craig P. Murphy, Ross D. Evans, Donagh P. Berry
Summary: This study detected SNP-phenotype imprinting associations for carcass weight, carcass conformation, and carcass fat in cattle. It identified imprinting associations at novel loci, and no known imprinted gene was found in these associations. The knowledge of these associations could be useful for improving genomic evaluations and mate allocation systems.
FRONTIERS IN GENETICS
(2022)
Review
Neurosciences
Cecilia Rocha, Panagiotis Prinos
Summary: Primary cilia play a critical role in directing cellular signaling events during brain development and neuronal differentiation. Genetic and epigenetic alterations, as well as RNA processing and post-translational modifications, contribute to the development of human neuronal disorders and brain tumors. This review summarizes research on mouse and human studies of ciliogenesis and primary cilia function in the brain, highlighting their role in maintaining neuronal progenitor populations, coordinating neuronal differentiation, and controlling key signaling pathways critical for neurogenesis. The impact of post-translational modifications and missplicing of ciliary genes leading to ciliopathies and cell cycle alterations is also discussed. Ultimately, genetic and epigenetic studies of cilia shed light on the cellular and molecular mechanisms underlying neurodevelopmental disorders and brain tumors.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Review
Behavioral Sciences
Dietrich van Calker, Tsvetan Serchov
Summary: Psychiatric disorders pose a significant burden on global healthcare systems, with genetic and epigenetic modifications potentially playing important roles in their pathogenesis. However, there is still limited understanding of these mechanisms, indicating a need for further research in this area.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2021)
Review
Immunology
Victor E. Nava, Pin-Yu Perera, Nirbhay Kumar, Maneesh Jain
Summary: Noncoding RNAs (ncRNAs) are RNA molecules that are not translated into protein but can convey information encoded in their DNA. Research on the exact function of ncRNAs is challenging but understanding their importance holds great potential for basic and translational research as well as therapeutic progress.
Article
Oncology
Foteinos-Ioannis Dimitrakopoulos, Anastasia Kottorou, Aspasia Tzezou
Summary: Breast cancer, the most common cancer in women, poses a challenge in therapeutic management for hormone receptor-positive patients due to resistance mechanisms. Molecular mechanisms involved in endocrine resistance include changes in hormone receptor signaling, activation of parallel pathways, cell cycle regulator modifications, transcription factor activation, and stem cell activity changes. Epigenetic changes, such as DNA methylation, histone modifications, and ncRNAs alterations, play a pivotal role not only in breast cancer progression but also in resistance to endocrine therapy.
Article
Multidisciplinary Sciences
Dhenugen Logeswaran, Yang Li, Khadiza Akhter, Joshua D. Podlevsky, Tamara L. Olson, Katherine Forsberg, Julian J-L Chen
Summary: A previously unknown messenger RNA-derived biogenesis pathway for telomerase RNA has been discovered in the basidiomycete fungus Ustilago maydis. This pathway involves the processing of a larger RNA precursor, which possesses mRNA characteristics, to produce a mature telomerase RNA. This finding expands our understanding of telomerase biogenesis mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Sebastian Bultmann, Stefan H. Stricker
Review
Neurosciences
Stefan H. Stricker, Magdalena Goetz
FRONTIERS IN NEUROSCIENCE
(2018)
Article
Biochemistry & Molecular Biology
Geoffrey J. Maher, Hannah K. Ralph, Zhihao Ding, Nils Koelling, Hana Mlcochova, Eleni Giannoulatou, Pawan Dhami, Dirk S. Paul, Stefan H. Stricker, Stephan Beck, Gilean McVean, Andrew O. M. Wilkie, Anne Goriely
Article
Biochemistry & Molecular Biology
Tjasa Lepko, Melanie Pusch, Tamara Mueller, Dorothea Schulte, Janina Ehses, Michael Kiebler, Julia Hasler, Hagen B. Huttner, Roosmarijn E. Vandenbroucke, Charysse Vandendriessche, Miha Modic, Ana Martin-Villalba, Sheng Zhao, Enric LLorens-Bobadilla, Anja Schneider, Andre Fischer, Christopher T. Breunig, Stefan H. Stricker, Magdalena Goetz, Jovica Ninkovic
Article
Multidisciplinary Sciences
Valentin Baumann, Maximilian Wiesbeck, Christopher T. Breunig, Julia M. Braun, Anna Koeferle, Jovica Ninkovic, Magdalena Goetz, Stefan H. Stricker
NATURE COMMUNICATIONS
(2019)
Review
Physiology
Christopher T. Breunig, Anna Koeferle, Andrea M. Neuner, Maximilian F. Wiesbeck, Valentin Baumann, Stefan H. Stricker
Summary: Despite knowing the potential genes that influence cell states, historical methods restricting manipulation of gene expression outside endogenous chromatin context have hindered understanding of how cells organize, interpret, and protect cellular programs. New methodological innovations are now providing opportunities to target and manipulate genomic and epigenomic loci for better understanding and manipulation of cellular states.
PHYSIOLOGICAL REVIEWS
(2021)
Review
Neurosciences
Stefan H. Stricker, Magdalena Goetz
Summary: The vulnerability of the mammalian brain lies in its limited ability to generate new neurons after maturation, but the direct conversion of non-neuronal cells to neurons offers a promising avenue for brain repair. Understanding the identity and chromatin hallmarks of induced neurons is crucial to avoid adverse effects and novel tools for manipulating specific epigenetic marks hold potential for erasing aberrant epigenetic memory and advancing therapeutic approaches for brain repair.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Cell & Tissue Engineering
Gianluca L. Russo, Giovanna Sonsalla, Poornemaa Natarajan, Christopher T. Breunig, Giorgia Bulli, Juliane Merl-Pham, Sabine Schmitt, Jessica Giehrl-Schwab, Florian Giesert, Martin Jastroch, Hans Zischka, Wolfgang Wurst, Stefan H. Stricker, Stefanie M. Hauck, Giacomo Masserdotti, Magdalena Goetz
Summary: Astrocyte-to-neuron conversion is a promising avenue for neuronal replacement therapy, with mitochondrial proteins playing a crucial role in the process. Early activation of genes encoding mitochondrial proteins significantly improves conversion efficiency, particularly for neuron-enriched antioxidant proteins.
Editorial Material
Cell Biology
Stefan H. Stricker, Benedikt Berninger, Magdalena Goetz
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2021)
Article
Cell Biology
Rosario Sanchez-Gonzalez, Christina Koupourtidou, Tjasa Lepko, Alessandro Zambusi, Klara Tereza Novoselc, Tamara Durovic, Sven Aschenbroich, Veronika Schwarz, Christopher T. Breunig, Hans Straka, Hagen B. Huttner, Martin Irmler, Johannes Beckers, Wolfgang Wurst, Andreas Zwergal, Tamas Schauer, Tobias Straub, Tim Czopka, Dietrich Truembach, Magdalena Goetz, Stefan H. Stricker, Jovica Ninkovic
Summary: The influx of cerebrospinal fluid after brain injury simultaneously activates toll-like receptor 2 (Tlr2) and chemokine receptor 3 (Cxcr3) pathways, leading to increased OPC proliferation and exacerbated glial reactivity. Interference with these pathways alleviated reactive gliosis, increased new neuron recruitment, and improved tissue restoration after injury.
Review
Biochemistry & Molecular Biology
Henrieta Papuchova, Paulina A. Latos
Summary: The placenta is crucial for the development of the embryo and the success of pregnancy. It serves as a site for exchange between the mother and the embryo, has immune functions, and acts as an important endocrine organ. Specialized trophoblast cell types, including syncytiotrophoblast and extravillous trophoblast, are responsible for these diverse functions of the placenta. Transcription factors play a vital role in regulating the emergence, specialization, and identity of these cells, and their coordinated actions determine the specific characteristics of each cell type. This article provides an overview of transcription factors involved in the development and function of human trophoblast and discusses their similarities and differences to their counterparts in mice. The establishment of human in vitro models combined with -omics approaches has greatly advanced our understanding of the human trophoblast field.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Sandra Haider, Andreas Ian Lackner, Bianca Dietrich, Victoria Kunihs, Peter Haslinger, Gudrun Meinhardt, Theresa Maxian, Leila Saleh, Christian Fiala, Juergen Pollheimer, Paulina A. Latos, Martin Knoefler
Summary: Comparative gene expression analysis revealed the importance of transforming growth factor-beta (TGF-beta) signaling in the development of extravillous trophoblasts (EVTs), particularly in the differentiation of placental EVTs into decidual EVTs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Bob A. Hersbach, David S. Fischer, Giacomo Masserdotti, Deeksha, Karolina Mojzisova, Thomas Waltzhoeni, Diego Rodriguez-Terrones, Matthias Heinig, Fabian J. Theis, Magdalena Goetz, Stefan H. Stricker
Summary: Collide-seq, a single-cell protocol, has shed light on the basic principles of fate erasure and cell identity conflict resolution in direct reprogramming. It revealed the lack of a common mechanism for the loss of fibroblast-specific gene expression and showed that the abrupt transcriptional changes in converting cells occur when critical levels of reprogramming factors are reached. The study also demonstrated that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Correction
Cell & Tissue Engineering
Gianluca L. Russo, Giovanna Sonsalla, Poornemaa Natarajan, Christopher T. Breunig, Giorgia Bulli, Juliane Merl-Pham, Sabine Schmitt, Jessica Giehrl-Schwab, Florian Giesert, Martin Jastroch, Hans Zischka, Wolfgang Wurst, Stefan H. Stricker, Stefanie M. Hauck, Giacomo Masserdotti, Magdalena Goetz
Article
Endocrinology & Metabolism
Sandra Haider, Magdalena Gamperl, Thomas R. Burkard, Victoria Kunihs, Ulrich Kaindl, Sini Junttila, Christian Fiala, Katy Schmidt, Sasha Mendjan, Martin Knoefler, Paulina A. Latos