Article
Multidisciplinary Sciences
Thomas Dahlet, Matthias Truss, Ute Frede, Hala Al Adhami, Anais F. Bardet, Michael Dumas, Judith Vallet, Johana Chicher, Philippe Hammann, Sarah Kottnik, Peter Hansen, Uschi Luz, Gonzalo Alvarez, Ghislain Auclair, Jochen Hecht, Peter N. Robinson, Christian Hagemeier, Michael Weber
Summary: During mouse development, the transcription factor E2F6 is crucial in targeting CpG island DNA methylation and epigenetic silencing to germline genes, especially in early embryonic cells. The cooperation between E2F6 and MGA is essential for silencing a subgroup of germline genes, dependent on the E2F6 marked box domain. E2F6 is required for initiating epigenetic silencing in early embryonic cells but becomes dispensable for maintenance in differentiated cells.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Daniel Matsusaka, Javier F. Botto, Diego H. Sanchez
Summary: This study reveals the central regulatory role of specific noncoding tandem repeats in the intersection between epigenetic silencing and gene expression, and their importance in plant stress responses.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Multidisciplinary Sciences
Nicolas Butel, Agnes Yu, Ivan Le Masson, Filipe Borges, Taline Elmayan, Christelle Taochy, Nial R. Gursanscky, Jiangling Cao, Shengnan Bi, Anne Sawyer, Bernard J. Carroll, Herve Vaucheret
Summary: The research reveals that there are discrepancies in the epigenetic behavior of transgenes and endogenous genes in Arabidopsis, indicating that they are regulated by different mechanisms.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Wenqiang Pan, Jingru Li, Yunpeng Du, Yajie Zhao, Yin Xin, Shaokun Wang, Chang Liu, Zhimin Lin, Shaozhong Fang, Yingdong Yang, Michele Zaccai, Xiuhai Zhang, Mingfang Yi, Sonia Gazzarrini, Jian Wu
Summary: Restoring intercellular communication is crucial for cell activity in buds during the transition from slow to fast growth in plants after dormancy release. However, the epigenetic regulation of this process is not well understood. This study shows that the lily gene LoVIL1 mediates plasmodesmata opening by repressing CALLOSE SYNTHASE 3 (LoCALS3) through epigenetic mechanisms. Furthermore, a transcription factor called LoNFYA7 recruits the LoVIL1-Polycomb Repressive Complex 2 (PRC2) to enhance H3K27me3 at the LoCALS3 locus, facilitating the growth transition in lily bulbs.
Article
Biochemistry & Molecular Biology
Gui-Xin Peng, Xue-Ling Mao, Yating Cao, Shi-Ying Yao, Qing-Run Li, Xin Chen, En-Duo Wang, Xiao-Long Zhou
Summary: The study found that mitochondrial aminoacyl-tRNA synthetases (mito aaRSs) partially colocalize with mitochondrial RNA granules (MRGs), possibly facilitated by their tRNA-binding capacity. Additionally, several mito aaRS-containing complexes were discovered, and their activities were influenced by interactions. These findings deepen our understanding of the functional and regulatory mechanisms of mito aaRSs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Victoria Cunha Alves, Joana Figueiro-Silva, Isidre Ferrer, Eva Carro
Summary: Modulation of brain olfactory (OR) and taste receptor (TASR) expression was found in neurological diseases, such as Alzheimer's disease (AD). In this study, the expression and regulation of OR and TASR were explored in the human orbitofrontal cortex (OFC) of sporadic AD patients. The results showed that the genes were downregulated at early stages of AD, suggesting transcriptional regulation through epigenetic mechanisms. The interaction between H3K9me3 and MeCP2 was also discovered, implicating MeCP2 in the transcriptional regulation of OR and TASR in AD.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Multidisciplinary Sciences
Gabriel K. Griffin, Jingyi Wu, Arvin Iracheta-Vellve, James C. Patti, Jeffrey Hsu, Thomas Davis, Deborah Dele-Oni, Peter P. Du, Aya G. Halawi, Jeffrey J. Ishizuka, Sarah Y. Kim, Susan Klaeger, Nelson H. Knudsen, Brian C. Miller, Tung H. Nguyen, Kira E. Olander, Malvina Papanastasiou, Suzanna Rachimi, Emily J. Robitschek, Emily M. Schneider, Mitchell D. Yeary, Margaret D. Zimmer, Jacob D. Jaffe, Steven A. Carr, John G. Doench, W. Nicholas Haining, Kathleen B. Yates, Robert T. Manguso, Bradley E. Bernstein
Summary: A CRISPR-Cas9 screen in mouse tumour models treated with immune checkpoint blockade identified SETDB1 as an epigenetic checkpoint protein that suppresses tumour-intrinsic immunogenicity. Loss of SETDB1 leads to derepression of immune-stimulating genes and triggers TE-specific cytotoxic T cell responses, suggesting it as a potential target for immunotherapy in cancer treatment.
Article
Medicine, Research & Experimental
Sheng-Chieh Hsu, Chia-Lin Chen, Mei-Ling Cheng, Cheng-Ying Chu, Chun A. Changou, Yen-Ling Yu, Shauh-Der Yeh, Tse-Chun Kuo, Cheng-Chin Kuo, Chih-Pin Chuu, Chien-Feng Li, Lu-Hai Wang, Hong-Wu Chen, Yun Yen, David K. Ann, Hung-Jung Wang, Hsing-Jien Kung
Summary: The study revealed the mechanisms of tumor cell death induced by arginine starvation, including suppression of gene expression, changes in metabolic profiles, and activation of immune responses. The dietary arginine-restriction model demonstrated that arginine starvation can suppress prostate cancer growth and enhance immune cell recruitment.
Article
Biochemistry & Molecular Biology
Arianna Di Fazio, Margarita Schlackow, Sheng Kai Pong, Adele Alagia, Monika Gullerova
Summary: In mammalian cells, a pathway called RNA interference (RNAi) uses small non-coding RNAs (sncRNAs) to negatively regulate gene expression. This study found that a specific type of sncRNA called tsRNA can promote gene silencing by targeting introns in the nucleus, which is different from the traditional post-transcriptional and transcriptional gene silencing mechanisms. Synthetic tsRNAs are able to significantly reduce the expression of target genes at both RNA and protein levels. This discovery has important implications for understanding gene regulation and developing novel therapeutic approaches.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Ali Seifinejad, Mergim Ramosaj, Ling Shan, Sha Li, Marie-Laure Possovre, Corinne Pfister, Rolf Fronczek, Lee A. Garrett-Sinha, David Frieser, Makoto Honda, Yoan Arribat, Dogan Grepper, Francesca Amati, Marie Picot, Andrea Agnoletto, Christian Iseli, Nicolas Chartrel, Roland Liblau, Gert J. Lammers, Anne Vassalli, Mehdi Tafti
Summary: Narcolepsy with cataplexy is caused by deficiency in the neuropeptide hypocretin/orexin (HCRT), believed to result from autoimmune destruction of hypocretin-producing neurons. Loss of hypothalamic CRH-producing neurons suggests that mechanisms other than autoimmune attack are involved. HCRT, PDYN, and CRH are epigenetically silenced by hypothalamic inflammation in narcolepsy patients, without concurrent cell death. Methylation reversal may lead to a potential cure for narcolepsy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Kaile Sun, Danny Schipper, Evert Jacobsen, Richard G. F. Visser, Francine Govers, Klaas Bouwmeester, Yuling Bai
Summary: The study found that genetic silencing of potato susceptibility genes can enhance resistance against late blight disease. Different mechanisms, including cell death responses and hormone-mediated signaling pathways, are involved in resistance mediated by different gene silencing.
HORTICULTURE RESEARCH
(2022)
Article
Immunology
Anna M. Masyutina, Polina V. Maximchik, Georgy Z. Chkadua, Mikhail V. Pashenkov
Summary: This study demonstrates that activation of TLR4 or NOD1 receptors leads to innate tolerance in macrophages. Epigenetic mechanisms have less impact on innate tolerance compared to signaling mechanisms. In NOD1-tolerized macrophages, responses to homologous restimulation are almost completely abolished, while LPS-tolerized macrophages retain partial activation of the NF-kappa B pathway to maintain low-level expression of pro-inflammatory genes. Additionally, most genes that become unresponsive to homologous stimuli show responses to agonists of receptors signaling via distinct pathways.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Plant Sciences
Nobutoshi Yamaguchi
Summary: This article summarizes the importance of gene regulatory networks in plant reproductive development and discusses the recent advances in utilizing genetic engineering and chemical application to modulate the epigenetic regulation of gene expression.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Evgenia Kupriyanova, Andrey Manakhov, Tatiana Ezhova
Summary: Plants can adjust their development in response to environmental changes by modifying the epigenomes of cells. The genes PARG1 and EXA1 in Arabidopsis are involved in maintaining leaf cell identity and play a role in controlling plant development through epigenetic regulation.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Biotechnology & Applied Microbiology
Wenhua Bao, Aoga Li, Yanan Zhang, Pengfei Diao, Qiqi Zhao, Ting Yan, Zikai Zhou, Huimin Duan, Xugang Li, Hada Wuriyanghan
Summary: The study introduces Host-induced gene silencing (HIGS) as a new strategy for pest control and demonstrates the successful application of transgenic plants targeting chitinase encoding genes in the maize pest Mythimna separata. The development of an artificial microRNA (amiR) based PTA system has significantly improved knockdown efficiency and caused more pronounced developmental abnormalities in recipient insects. Common features and differences in siRNA characteristics after HIGS and direct dsRNA/siRNA feeding are analyzed, along with the identification of core RNAi genes in M. separata. The study provides compelling evidence for the potential use of the PTA system in future RNAi control of lepidopteran pests.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Stephanie Lalande, Remy Merret, Thalia Salinas-Giege, Laurence Drouard
Article
Cell Biology
Mickaele Hemono, Elodie Ubrig, Kevin Azeredo, Thalia Salinas-Giege, Laurence Drouard, Anne-Marie Duchene
Article
Biochemistry & Molecular Biology
Jessica M. Warren, Thalia Salinas-Giege, Guillaume Hummel, Nicole L. Coots, Joshua M. Svendsen, Kristen C. Brown, Laurence Drouard, Daniel B. Sloan
Summary: Differences in tRNA expression play a crucial role in biological processes, but measuring abundance and detecting modifications remains challenging. Researchers modified standard RNA-seq methods to sequence tRNAs from flowering plants and produced a modification index, revealing insights into tRNA modifications.
Review
Biochemistry & Molecular Biology
Kateryna Fal, Denisa Tomkova, Gilles Vachon, Marie-Edith Chaboute, Alexandre Berr, Cristel C. Carles
Summary: This review discusses the advantages and limitations of tools and technologies developed for impacting epigenetic marks in functional epigenomics. The methods range from drug inhibitors and nanobodies to engineered proteins targeting specific chromatin regions, with recent developments focusing on more precise and flexible tool designs. Proof-of-concept studies also indicate future potential for even finer, inducible/switchable systems for temporal analyses of molecular events following changes in chromatin marks.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Thalia Salinas-Giege, Elodie Ubrig, Laurence Drouard
Summary: Mitochondria have evolved considerably since originating from a single endosymbiosis event, acquiring unique traits in different eukaryotic kingdoms. The freshwater alga Cyanophora paradoxa serves as an exciting model for studying the evolution of mitochondrial gene expression, showing that tRNAs can function in mRNA processing in a non-conventional manner. The tRNA-like elements found in the 3'-terminals of mitochondrial mRNAs in land plants are proposed to originate from true tRNAs found in the mitochondria of basal photosynthetic glaucophyte.
Article
Biochemistry & Molecular Biology
Elizabeth Ramos-Morales, Efil Bayam, Jordi Del-Pozo-Rodriguez, Thalia Salinas-Giege, Martin Marek, Peggy Tilly, Philippe Wolff, Edouard Troesch, Eric Ennifar, Laurence Drouard, Juliette D. Godin, Christophe Romier
Summary: This study provides insights into the molecular mechanisms of tRNA deamination by ADAT2 and the importance of the ADAT3 N-terminal domain in tRNA binding and deamination. The rotation of the N-terminal domain with respect to the catalytic domain plays a crucial role in presenting and positioning the tRNA anticodon-stem-loop correctly in the ADAT2 active site. A founder mutation in the ADAT3 N-terminal domain, causing intellectual disability, is shown to hinder optimal presentation of the tRNA anticodon-stem-loop to ADAT2.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Plant Sciences
Katherine Domb, Nan Wang, Guillaume Hummel, Chang Liu
Summary: The high-throughput sequencing-based methods have significantly advanced the study of chromatin and provided new insights into plant spatial genome structures and different levels of organization. The complexity of organellar genomes and their 3D packing into nucleoids have also been addressed in the research.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Florent Waltz, Thalia Salinas-Giege, Robert Englmeier, Herrade Meichel, Heddy Soufari, Lauriane Kuhn, Stefan Pfeffer, Friedrich Forster, Benjamin D. Engel, Philippe Giege, Laurence Drouard, Yaser Hashem
Summary: The study explores the structural and species-specific adaptations of the mitochondrial ribosome in Chlamydomonas reinhardtii, shedding light on the extreme diversity of mitoribosomes and their membrane tethering strategies.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Yihan Dong, Veli V. Uslu, Alexandre Berr, Gaurav Singh, Csaba Papdi, Victor A. Steffens, Thierry Heitz, Lyubov A. Ryabova
Summary: The target of rapamycin (TOR) acts as a central sensory hub connecting external stimuli to gene expression. The mechanism for stimulus-specific transcriptional reprogramming by TOR is not well understood. In this study, we analyzed Arabidopsis in silico and found that TOR-repressed genes are associated with bistable or silent chromatin states. These chromatin states are regulated by histone modifications, particularly H3K27me3, and the combination of H3K4me3 and H3K27me3 allows rapid transcriptional changes in response to stimuli.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Kateryna Fal, Alexandre Berr, Marie Le Masson, Adi Faigenboim, Emeline Pano, Nickolay Ishkhneli, Netta-Lee Moyal, Claire Villette, Denisa Tomkova, Marie-Edith Chaboute, Leor Eshed Williams, Cristel C. Carles
Summary: Chromatin is a dynamic platform that regulates gene expression through epigenetic modifications, particularly targeting histone H3 amino acid residues. This study focuses on the function of lysine 27 of H3 (H3K27), specifically its trimethylation by the Polycomb Repressive Complex 2 (PRC2), in controlling developmental genes in plants. By expressing a non-modifiable variant of H3 at residue K27 (H3.3(K27A)) in Arabidopsis, the researchers discovered novel roles of H3K27 in plant cell fates, metabolic pathways, and the elongation and lignin composition of the stem.
Review
Plant Sciences
Gilles Dupouy, Yihan Dong, Etienne Herzog, Marie-Edith Chaboute, Alexandre Berr
Summary: The nucleus is a central organelle in eukaryotic cells that undergoes dynamic structural changes during cellular processes. This review focuses on recent data obtained in plants, particularly in response to mechanical stress, and highlights the similarities and differences between animal and plant cells in terms of nuclear envelope dynamics and functional impacts.
Article
Biochemistry & Molecular Biology
Jessica M. Warren, Thalia Salinas-Giege, Deborah A. Triant, Douglas R. Taylor, Laurence Drouard, Daniel B. Sloan
Summary: Research on mitochondrial genomes of Silene plants reveals the process of tRNA gene loss and replacement, as well as the import of nuclear-encoded tRNAs. Even in systems with recent mitochondrial tRNA gene loss, nuclear-encoded counterparts may likely replace mitochondrial tRNAs, providing insight into the evolutionary history of plant mitochondrial genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)