Article
Plant Sciences
Naoki Takahashi, Kazuki Suita, Toshiya Koike, Nobuo Ogita, Ye Zhang, Masaaki Umeda
Summary: In Arabidopsis roots, the brassinosteroid receptor BRL3 plays a major role in activating QC division in response to DNA double-strand breaks, with the involvement of the transcription factor ETHYLENE RESPONSE FACTOR 115. This study reveals that DNA double-strand breaks promote regenerative cell division at the quiescent center by elevating the expression of BRL3.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Matej Lexa, Monika Cechova, Son Hoang Nguyen, Pavel Jedlicka, Viktor Tokan, Zdenek Kubat, Roman Hobza, Eduard Kejnovsky
Summary: This article introduces a novel approach to analyze the role of repetitive elements in the 3D organization of genomes. By combining Hi-C data, reference genome data, and tools for repeat analysis, a pipeline was constructed to identify and quantify the contacts between specific repeat families, generating heatmaps and circular diagrams for visualization. Using this pipeline with tomato data, preferential homotypic interactions of ribosomal DNA, centromeric satellites, and some LTR retrotransposon families were revealed.
Article
Cell Biology
Zhipeng Ai, Xinyu Xiang, Yangquan Xiang, Iwona Szczerbinska, Yuli Qian, Xiao Xu, Chenyang Ma, Yaqi Su, Bing Gao, Hao Shen, Muhammad Nadzim Bin Ramli, Di Chen, Yue Liu, Jia-jie Hao, Huck Hui Ng, Dan Zhang, Yun-Shen Chan, Wanlu Liu, Hongqing Liang
Summary: This study reveals the mechanism of specific activation of ERVs during human embryonic development, indicating that ERVs are activated by cell-state-specific transcription machinery and contribute to stage-specific transcription network and cell potency.
Review
Plant Sciences
Nathan S. Catlin, Emily B. Josephs
Summary: TEs play a significant role in genomic variation in plants. New approaches have allowed us to quantify TE polymorphisms and understand their evolutionary dynamics, revealing their important but underappreciated contribution to intraspecific phenotypic variation.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hangxia Jin, Xujun Fu, Xiaomin Yu, Longming Zhu, Qinghua Yang, Fengjie Yuan
Summary: This study considered for the first time the effects of transposon alterations in soybean caused by space mutation. Comparative analysis of a new soybean variety derived from space mutation treatment and its parent soybean revealed significant structural differences and differential genes related to defense response, cell wall-related processes, and epigenetics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Renata Orlowska, Katarzyna A. Pachota, Wioletta M. Dynkowska, Agnieszka Niedziela, Piotr T. Bednarek
Summary: Transposable elements (TEs) in plant genomes may be activated under stress, leading to DNA sequence variation. In vitro plant regeneration can induce changes in DNA methylation levels, affecting the activation of TEs and DNA sequence variation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Maria Isabel Navarro-Mendoza, Carlos Perez-Arques, Joseph Heitman
Summary: Chromatin modifications, specifically H3K9 methylation, play a crucial role in repressing transcription in early-diverging fungi. RNA interference (RNAi) and heterochromatin formation are independent regulatory mechanisms in Mucor, contributing to genome stability and defense.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Yan Jin, Yunkun Lu, Lianyu Lin, Chao Liu, Xiaojie Ma, Xi Chen, Ziyu Zhou, Zhensheng Hu, Jiaqi Pu, Guo Chen, Qian Deng, Liling Jiang, Yuhan Li, Yulong Zhao, Hao Wang, Junfen Fu, Wei Li, Saiyong Zhu
Summary: Chemistry-alone approach has been used to initiate pluripotency in somatic cells, but it has low efficiency and lacks understanding of the underlying mechanisms. This study reveals that the small molecule CD3254 activates the transcription factor RXRa and promotes chemical reprogramming in mice. The CD3254-RXRa-RNA exosome axis directly activates RNA exosome component genes, leading to the degradation of transposable element-associated RNAs and reduction of TE-mediated inflammation, ultimately promoting successful reprogramming.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Patrick J. Flynn, Peter D. Koch, Timothy J. Mitchison
Summary: Mitotic errors can activate cGAS and induce IFN signaling through the formation of chromatin bridges, which are selectively generated by microtubule stabilizers and MPS1 inhibitors. These chromatin bridges activate cGAS and lead to the transfer of 20 30-cGAMP between cells, suggesting a potential mechanism for immunosurveillance of cells that fail mitosis and antitumor actions of taxanes and MPS1 inhibitors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Camille Cornet, Pablo Mora, Hannah Augustijnen, Petr Nguyen, Marcial Escudero, Kay Lucek
Summary: Repetitive elements can cause large-scale chromosomal rearrangements, potentially promoting reproductive isolation and speciation. The role of repetitive elements in holocentric organisms and their association with karyotype changes in Erebia butterflies and Carex sedges were investigated at both micro- and macro-evolutionary scales. The results suggest that repetitive elements are associated with population differentiation and chromosomal rearrangements in holocentric clades, playing a role in adaptation and species diversification.
Review
Cell Biology
Melody Nicolau, Nathalie Picault, Guillaume Moissiard
Summary: Transposable elements (TEs) are self-replicating DNA elements that make up major fractions of eukaryote genomes. Host cells have developed strategies to repress TE activity, including epigenetic pathways. TE exaptation refers to the phenomenon of host utilizing TE-derived sequences for adaptive benefits.
Review
Biochemistry & Molecular Biology
Aleksander Lipszyc, Magdalena Szuplewska, Dariusz Bartosik
Summary: The emerging phenomenon of antibiotic resistance poses a significant threat to the effectiveness of antibacterial therapies. Horizontal gene transfer mediated by mobile genetic elements, such as transposable elements, plays a major role in disseminating resistance between phylogenetically distant bacterial species. These elements can mobilize adjacent genes and activate transcriptionally silent genetic information, potentially converting dormant genes into fully functional antibiotic resistance determinants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Maria Tokuyama, Bronwyn M. Gunn, Arvind Venkataraman, Yong Kong, Insoo Kang, Tasfia Rakib, Michael J. Townsend, Karen H. Costenbader, Galit Alter, Akiko Iwasaki
Summary: In this study, elevated expression of an endogenous retrovirus ERV-K102, encoding an envelope protein, was observed in the blood of SLE patients, correlating with autoantibody levels and higher interferon status. Induction of ERV-K102 in SLE was negatively correlated with the expression of epigenetic silencing factors. Anti-ERV-K102 IgG levels in SLE plasma correlated with higher interferon stimulated gene expression, and promoted enhanced neutrophil phagocytosis of ERV-K102 envelope protein through immune complex formation.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Review
Genetics & Heredity
Dana Larocca, Jieun Lee, Michael D. West, Ivan Labat, Hal Sternberg
Summary: Multicellular life evolved from replicating unicellular organisms into two different cell types: immortal germline and mortal soma controlled by DNA clocks. Aging is caused by the progressive limitation of growth and regeneration in somatic cells. Reprogramming may lead to therapeutic strategies to alter aging and treat degenerative diseases.
Review
Biotechnology & Applied Microbiology
Yuxin Pan, Yuhui Zhuang, Tao Liu, Hua Chen, Lihui Wang, Rajeev K. Varshney, Weijian Zhuang, Xiyin Wang
Summary: Peanut is a globally important oil and protein crop with a large genome. The sequencing of diploid and tetraploid peanut genomes has provided insights into their genome structures, evolution, and biological characteristics. The sequencing efforts revealed a subgenome bias in gene retention and gene expression, which may be related to LTR explosions after tetraploidization. Important genes, such as those involved in fatty acid and triacylglycerol pathways, NBS-LRR, and seed size determination, were found to be enriched after polyploidization events. The genome sequencing achievement has laid a solid foundation for advancing peanut crop enhancement and systems biology research, despite peanut lagging behind other crops in terms of genomic resources.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biology
Manutea C. Serrero, Virginie Girault, Sebastian Weigang, Todd M. Greco, Ana Ramos-Nascimento, Fenja Anderson, Antonio Piras, Ana Hickford Martinez, Jonny Hertzog, Anne Binz, Anja Pohlmann, Ute Prank, Jan Rehwinkel, Rudolf Bauerfeind, Ileana M. Cristea, Andreas Pichlmair, Georg Kochs, Beate Sodeik, Adam P. Geballe
Summary: This study identifies an interferon-inducible protein, MxB, that can sense herpesviral capsids and disassemble them, thereby restricting viral nuclear targeting and progeny capsid assembly, leading to enhanced innate immune responses.
Article
Biochemistry & Molecular Biology
Jonny Hertzog, Wen Zhou, Gerissa Fowler, Rachel E. Rigby, Anne Bridgeman, Henry Tw Blest, Chiara Cursi, Lise Chauveau, Tamara Davenne, Benjamin E. Warner, Paul R. Kinchington, Philip J. Kranzusch, Jan Rehwinkel
Summary: Varicella-Zoster virus (VZV) infection induces type I interferon (IFN) production through the cGAS/STING DNA sensing pathway, while VZV tegument protein ORF9 functions as an antagonist of cGAS, restricting VZV replication.
Article
Biology
Tobias Moll, Valerie Odon, Calum Harvey, Mark O. Collins, Andrew Peden, John Franklin, Emily Graves, Jack N. G. Marshall, Cleide dos Santos Souza, Sai Zhang, Lydia Castelli, Guillaume Hautbergue, Mimoun Azzouz, David Gordon, Nevan Krogan, Laura Ferraiuolo, Michael P. Snyder, Pamela J. Shaw, Jan Rehwinkel, Johnathan Cooper-Knock
Summary: This study identifies a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. Increased expression of EXOSC2 is associated with higher risk of clinical COVID-19. The study also reveals interaction between the SARS-CoV-2 RNA polymerase and most of the human RNA exosome components.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemical Research Methods
Jonny Hertzog, Jan Rehwinkel
Summary: A transwell-based infection system was developed to study the molecular and cellular biology of Varicella-Zoster virus (VZV) without mixed cell populations. This simple method allows for infection of various target cells and provides pure cell populations for downstream analyses.
JOURNAL OF VIROLOGICAL METHODS
(2023)
Article
Multidisciplinary Sciences
Isabell Hess, Sagar, Connor O'Meara, Dominic Gruen, Michael Schorpp, Thomas Boehm
Summary: The zinc finger transcription factor Ikzf1 plays an important role in lymphoid development in mammals. This study investigates the phenotypes of zebrafish homozygous for two different mutant ikzf1 alleles. The results show that the mutants exhibit increased myelopoiesis and stimulate erythroid differentiation, suggesting a stage-specific function of ikzf1 in regulating hematopoiesis.
SCIENTIFIC REPORTS
(2022)
Article
Hematology
Megan Walker, Yichao Li, Antonio Morales-Hernandez, Qian Qi, Chaithanyarani Parupalli, Scott Brown, Claiborne Christian, Wilson K. Clements, Yong Cheng, Shannon McKinney-Freeman
Summary: NFIX is a positive regulator of hematopoietic stem and progenitor cell (HSPC) transplantation. The absence of NFIX leads to loss of HSPCs and accumulation of specific cell types. NFIX collaborates with PU.1 at super-enhancers to regulate genes involved in cellular respiration and hematopoietic differentiation. NFIX deficiency negatively affects PU.1 binding at certain genomic loci.
Article
Gastroenterology & Hepatology
Hendrik Luxenburger, David B. Reeg, Julia Lang-Meli, Matthias Reinscheid, Miriam Eisner, Dominik Bettinger, Valerie Oberhardt, Elahe Salimi Alizei, Katharina Wild, Anne Graeser, Vivien Karl, Sagar, Florian Emmerich, Florian Klein, Marcus Panning, Daniela Huzly, Bertram Bengsch, Tobias Boettler, Roland Elling, Robert Thimme, Maike Hofmann, Christoph Neumann-Haefelin
Summary: Liver transplant recipients have a reduced immune response to COVID-19 mRNA vaccination, especially after the third (and fourth) vaccine dose, and the interaction between humoral and cellular immunity is not well understood.
JOURNAL OF HEPATOLOGY
(2023)
Editorial Material
Cell Biology
Effie Apostolou, Helen Blau, Kenneth Chien, Madeline A. Lancaster, Purushothama Rao Tata, Eirini Trompouki, Fiona M. Watt, Yi Arial Zeng, Magdalena Zernicka-Goetz
Summary: Since the discovery of stem cells, researchers have identified unique abilities of self-renewal and differentiation toward diverse cell types in different organs. Stem cells have become a promising tool in therapeutics and stem cell biology is rapidly evolving. In this article, stem cell biologists share their perspectives on the most notable advances and challenges in the field.
NATURE CELL BIOLOGY
(2023)
Article
Microbiology
Elisa Dell'Aglio, Virginie Lacotte, Sergio Peignier, Isabelle Rahioui, Fadela Benzaoui, Agnes Vallier, Pedro Da Silva, Emmanuel Desouhant, Abdelaziz Heddi, Rita Rebollo
Summary: Beetles rely on endosymbionts to synthesize aromatic amino acids that reinforce their protective cuticle. The exponential increase in endosymbiotic titer observed in Sitophilus oryzae/Sodalis pierantonius interaction is triggered by host carbohydrate intake. Host survival and cuticle biosynthesis are influenced by the nutritional status and food quality and availability.
Article
Physiology
Mariana Galvao Ferrarini, Agnes Vallier, Elisa Dell'Aglio, Severine Balmand, Carole Vincent-Monegat, Meriem Debbache, Justin Maire, Nicolas Parisot, Anna Zaidman-Remy, Abdelaziz Heddi, Rita Rebollo
Summary: Insects establish long-term relationships with intracellular symbiotic bacteria, which provide them with essential nutrients. The endosymbionts are confined within specialized host cells called bacteriocytes, which form the bacteriome organ. In the cereal weevil Sitophilus oryzae, bacteriomes are present at specific locations in larvae and adults. While the midgut bacteriomes experience proliferation and elimination, the ovarian bacteriomes are maintained throughout the weevil's lifetime. Ovarian endosymbionts are thought to be transmitted through the female germline, but the exact mode of transmission is not fully understood.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Virginie Lacotte, Elisa Dell'Aglio, Sergio Peignier, Fadela Benzaoui, Abdelaziz Heddi, Rita Rebollo, Pedro Da Silva
Summary: In this study, we investigated the potential of Hyperspectral Imaging (HSI) as a standardized cuticle analysis tool for studying insect cuticle changes. We demonstrated the reliability and feasibility of HSI by comparing its results with the traditionally used Red-Green-Blue analysis. We assessed the phenotypic changes of cereal weevils under different diets and highlighted the assets of HSI for developing a simple, automated, and standardized analysis tool in laboratory conditions.
Article
Cell Biology
Katrin M. Schuele, Jelena Weckerle, Simone Probst, Alexandra E. Wehmeyer, Lea Zissel, Chiara M. Schroeder, Mehmet Tekman, Gwang-Jin Kim, Inga-Marie Schlaegl, Sagar, Sebastian J. Arnold
Summary: Eomes and Brachyury exhibit distinct transcriptional activities, guiding the specification of specific cell lineages. While their binding sites overlap at the promoters of target genes, they show specificity for distal enhancer regions.
DEVELOPMENTAL CELL
(2023)
Article
Cell Biology
Eline Lemerle, Eirini Trompouki
Summary: Transposable elements (TEs) are dispersed repetitive DNA sequences that can move within a genome. Despite their inability to transpose due to mutations, TEs still play important roles in hematopoiesis, innate immune sensing, inflammation, and disease. Further studies into the function of TEs in the hematopoietic system are crucial for therapeutic manipulation.
DISEASE MODELS & MECHANISMS
(2023)
Review
Immunology
Jonathan Maelfait, Jan Rehwinkel
Summary: ZBP1 is a sensor that recognizes double-stranded nucleic acids in the unusual Z conformation. It plays multifaceted roles in disease pathology by inducing regulated cell death and proinflammatory signaling. ZBP1 is involved in antiviral defense, autoinflammation, cancer, and emerging as a potential therapeutic target.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Endocrinology & Metabolism
Ev-Marie Schuster, Maximilian W. Epple, Katharina M. Glaser, Michael Mihlan, Kerstin Lucht, Julia A. Zimmermann, Anna Bremser, Aikaterini Polyzou, Nadine Obier, Nina Cabezas-Wallscheid, Eirini Trompouki, Andrea Ballabio, Joerg Vogel, Joerg M. Buescher, Alexander J. Westermann, Angelika S. Rambold
Summary: There is a metabolic pathway regulated by TFEB between phago-lysosomes and mitochondria in macrophages, which restricts the growth of Salmonella bacteria by producing itaconate.