Editorial Material
Biochemistry & Molecular Biology
Marc Graille
Summary: This study presents the crystal structure of the complex formed by eukaryotic ERH protein and a short peptide of its partner, providing valuable insights into the different biological functions governed by this highly conserved protein family.
Review
Neurosciences
Xiaobing Huang, Garry Wong
Summary: PIWI-interacting RNAs (piRNAs) are small and highly conserved non-coding transcripts that regulate gene expression to maintain genome stability. They play roles not only in protecting against transposable element invasion but also in sterility, tumorigenesis, metabolic homeostasis, neurodevelopment, and neurodegenerative diseases.
TRANSLATIONAL NEURODEGENERATION
(2021)
Article
Plant Sciences
Jay Shockey, Matthew K. Gilbert, Gregory N. Thyssen
Summary: Researchers successfully identified a mutant allele in a fatty acid desaturase gene that is responsible for the high oleic acid content in certain cotton accessions. They also found that the missing amino acid residues in the mutant protein are not essential for enzyme activity but are necessary for proper subcellular targeting. This discovery will facilitate breeding programs to introduce the high oleic acid trait into other cotton varieties.
Article
Biology
Marzia Munafo, Victoria R. Lawless, Alessandro Passera, Serena MacMillan, Susanne Bornelov, Irmgard U. Haussmann, Matthias Soller, Gregory J. Hannon, Benjamin Czech
Summary: The nuclear pore complex (NPC) functions as a gateway between the nucleus and cytoplasm for exchange of macromolecular cargo. Specific nucleoporins within the NPC, such as Nup54 and Nup58, have essential roles in transposon silencing via the piRNA pathway in the Drosophila ovary, suggesting tissue-specific functions for certain NPC subunits. This study demonstrates that genomic loci under selective pressure can exploit NPC subunits to facilitate their expression, indicating additional functions beyond nuclear/cytoplasmic exchange for the NPC.
Article
Cell Biology
Masaki Kawase, Kenji Ichiyanagi
Summary: In mammals, germ cells produce small regulatory RNAs called piRNAs, which have different characteristics and expression dynamics during development. The length of piRNAs is correlated with PIWI-like proteins, and retrotransposon-derived piRNAs are abundantly produced but decline in abundance as development proceeds.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
S. Horjales, M. Li Calzi, M. E. Francia, A. Cayota, M. R. Garcia-Silva
Summary: piRNAs function as genome defense mechanisms against transposable elements insertions within germ line cells, and recent studies have revealed their presence in non-gonadal somatic contexts. The presence of piRNA pathways has also been reported in bacteria, mollusks, and arthropods, with various functions including genome protection, gene expression regulation, and axon regeneration. In parasitic protozoa, the presence of PIWI-related machinery suggests the existence of an ancestral piRNA machinery that evolved in multicellular eukaryotes. Understanding current and ancestral PIWI/piRNAs will provide insights into genome integrity conservation and host defense mechanisms by protozoan parasites.
FRONTIERS IN GENETICS
(2023)
Article
Biology
Xuanzeng Liu, Muhammad Majid, Hao Yuan, Huihui Chang, Lina Zhao, Yimeng Nie, Lang He, Xiaojing Liu, Xiaoting He, Yuan Huang
Summary: Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway is underexpressed in the gigantic genome grasshopper. This may lead to the proliferation of transposable elements (TEs) and contribute to the gigantism of grasshopper genomes.
Article
Multidisciplinary Sciences
Matthew A. Lawlor, Weihuan Cao, Christopher E. Ellison
Summary: By reanalyzing single-cell RNA-seq datasets of Drosophila testis, researchers found that a distinct population of early spermatocytes expresses a large number of transposable elements (TEs) at much higher levels than other cell types, potentially achieving high insertional activity by exploiting the activation of Y chromosome-specific transcriptional programs.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Shengming Yang, Megan Overlander, Jason Fiedler
Summary: This study characterized and genetically mapped the gpa1.a mutation causing variegation in barley, identifying a potential candidate gene for Gpa1 in the PTOX-encoding gene in a delimited region. The findings provide a foundation for cloning Gpa1 and enhancing understanding of molecular mechanisms underlying chloroplast biogenesis in monocot plants.
Article
Multidisciplinary Sciences
Maya Spichal, Bree Heestand, Katherine Kretovich Billmyre, Stephen Frenk, Craig C. Mello, Shawn Ahmed
Summary: The sterility of the C. elegans Piwi prg-1 mutant is not associated with transposon-induced DNA damage, but is instead associated with and phenocopied by dysfunction of germ granules.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Jie Wang, Liang Yuan, Jiaxing Tang, Jiongyu Liu, Cheng Sun, Michael W. Itgen, Guiying Chen, Stanley K. Sessions, Guangpu Zhang, Rachel Lockridge Mueller
Summary: Transposable elements (TEs) and the silencing machinery of their hosts play a critical role in shaping genome size through a germline arms-race dynamic. This study investigates TE silencing pathways in the gonads of Ranodon sibiricus, which has a large genome size. The results indicate a significant relationship between piRNA expression and TE silencing, suggesting comprehensive piRNA-mediated silencing. Additionally, the study finds no association between TE silencing pathway gene expression and genome size in various vertebrates.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Maria Placentino, Antonio Miguel de Jesus Domingues, Jan Schreier, Sabrina Dietz, Svenja Hellmann, Bruno F. M. de Albuquerque, Falk Butter, Rene F. Ketting
Summary: In Caenorhabditis elegans, the piRNA (21U RNA) pathway is crucial for establishing proper gene regulation and an immortal germline. Maternally provided 21U RNAs can trigger RNA-induced epigenetic gene silencing (RNAe) in embryos. Furthermore, PID-2, a protein with intrinsically disordered regions, is essential for establishing and maintaining RNAe, and interacts with eTudor domain-containing proteins PID-4 and PID-5.
Article
Engineering, Environmental
Xiaoxian Xie, Jiafeng Zhou, Luting Hu, Ruonan Shu, Mengya Zhang, Lei Sun, Fengchun Wu, Zhengwei Fu, Zezhi Li
Summary: This study investigated the toxicological effects of Hexafluoropropylene oxide trimer acid (HFPO-TA) on mitochondrial function and biogenesis. Results showed that exposure to HFPO-TA induced adverse physiological changes in mice and was associated with disrupted mitochondrial energy metabolism.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Multidisciplinary Sciences
Xiaobing Huang, Changliang Wang, Tianjiao Zhang, Rongzhen Li, Liang Chen, Ka Lai Leung, Merja Lakso, Qinghua Zhou, Hongjie Zhang, Garry Wong
Summary: PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that play important roles in regulating gene expression and neurodegeneration. This study found dysregulated expression of piRNAs in disease models and brain samples of Parkinson's disease patients, suggesting their involvement in the pathogenesis of Lewy body diseases. The results provide insights into the molecular mechanisms underlying neurodegenerative disorders.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Daewon Kim, Jiyuan Yang, Fangwei Gu, Sungjin Park, Jonathon Combs, Alexander Adams, Heather B. Mayes, Su Jeong Jeon, Jeong Dong Bahk, Erik Nielsen
Summary: This study identified a temperature-sensitive root hair mutant, feronia-temperature sensitive (fer-ts), through genetic screening and mapping, revealing a temperature-dependent regulation mechanism for root hair formation.
Article
Cell Biology
Mehmet E. Karasu, Nora Bouftas, Scott Keeney, Katja Wassmann
JOURNAL OF CELL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Cynthia Petrillo, Vilma Barroca, Jonathan Ribeiro, Nathalie Lailler, Gabriel Livera, Scott Keeney, Emmanuelle Martini, Devanshi Jain
Article
Cell Biology
Shintaro Yamada, Anjali Gupta Hinch, Hisashi Kamido, Yongwei Zhang, Winfried Edelmann, Scott Keeney
GENES & DEVELOPMENT
(2020)
Article
Multidisciplinary Sciences
Hajime Murakami, Isabel Lam, Pei-Ching Huang, Jacquelyn Song, Megan van Overbeek, Scott Keeney
Article
Biochemistry & Molecular Biology
Anjali Gupta Hinch, Philipp W. Becker, Tao Li, Daniela Moralli, Gang Zhang, Clare Bycroft, Catherine Green, Scott Keeney, Qinghua Shi, Benjamin Davies, Peter Donnelly
Article
Biochemistry & Molecular Biology
Corentin Claeys Bouuaert, Sam E. Tischfield, Stephen Pu, Eleni P. Mimitou, Ernesto Arias-Palomo, James M. Berger, Scott Keeney
Summary: The study provides molecular analysis of the Saccharomyces cerevisiae Spo11 core complex and reveals structural and functional similarities with ancestral Topo VI. The Spo11 complex is found to be monomeric and exhibits topoisomerase-like DNA binding preferences, showing high affinity for DNA ends mimicking cleavage products. Mutations that reduce DNA binding in vitro lead to attenuated DSB formation and alterations in DSB processing and landscape in vivo.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Review
Genetics & Heredity
Hajime Murakami, Xiaojing Mu, Scott Keeney
Summary: The study shows that in budding yeast, the programmed formation of DNA double-strand breaks in meiotic prophase I is achieved through the targeted binding of DSB proteins on short chromosomes. This preferential binding is promoted by intrinsic features independent of the meiosis-specific cohesin subunit Rec8 and DNA replication.
Article
Multidisciplinary Sciences
Corentin Claeys Bouuaert, Stephen Pu, Juncheng Wang, Cedric Oger, Dima Daccache, Wei Xie, Dinshaw J. Patel, Scott Keeney
Summary: This study elucidates how Saccharomyces cerevisiae RMM proteins self-assemble on chromosome axes to create centers of DSB activity. Protein-DNA interactions drive condensation and recruitment of Spo11 complexes, highlighting the multilayered control of Spo11 in chromosome segregation.
Article
Multidisciplinary Sciences
Dominic Johnson, Margaret Crawford, Tim Cooper, Corentin Claeys Bouuaert, Scott Keeney, Bertrand Llorente, Valerie Garcia, Matthew J. Neale
Summary: Genetic recombination during meiosis involves the repair of DNA double-strand breaks (DSBs) created by Spo11, with recent findings indicating the existence of multiple Spo11 DSBs termed 'double cuts'. These double cuts vary in length with a periodicity of 10.5 base pairs and play a role in recombination and DNA gap repair during meiosis.
Article
Biochemistry & Molecular Biology
Agnieszka Lukaszewicz, Julian Lange, Scott Keeney, Maria Jasin
Summary: Numerous DNA double-strand breaks arise during meiosis to initiate homologous recombination. A distinct type of mutational event involves deletions formed by joining ends from closely spaced DSBs within single or adjacent hotspots. In the absence of the ATM kinase, these deletions are more frequent and may lead to insertional mutagenesis.
Article
Cell Biology
Yuhki Saito, Ben R. Hawley, M. Rhyan Puno, Shreya N. Sarathy, Christopher D. Lima, Samie R. Jaffrey, Robert B. Darnell, Scott Keeney, Devanshi Jain
Summary: In this study, the researchers investigated how the N-6-methyladenosine (m(6)A) reader and RNA helicase YTHDC2 regulate gene expression during meiosis. They found that YTHDC2 can bind transcripts independent of m(6)A status and regulate gene expression through distinct mechanisms during multiple stages of meiosis. Mutation of the m(6)A-binding pocket of YTHDC2 had no effect on gametogenesis, suggesting that YTHDC2's function is m(6)A-independent. However, mutation in the ATPase motif of YTHDC2 blocked meiotic prophase I progression, causing sterility.
GENES & DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Kaku Maekawa, Shintaro Yamada, Rahul Sharma, Jayanta Chaudhuri, Scott Keeney
Summary: This study demonstrates that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-seq method. Prominent clusters of S1-seq reads that coincide with H-DNA motifs and correlate strongly with the triplex-forming potential were observed in genomic DNA isolated from mouse testis cells and splenic B cells. The study further explores how the structure of H-DNA is modified by polypyrimidine repeat length and the presence of repeat-interrupting substitutions using naturally occurring H-DNA motifs across the mouse genome.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Kaixian Liu, Emily M. Grasso, Stephen Pu, Mengyang Zou, Shixin Liu, David Eliezer, Scott Keeney
Summary: This study reports the structure and dynamic DNA binding properties of the Rec114 and Mei4 protein complex, which initiates DNA double-strand breaks during meiotic recombination. The complex can bridge multiple DNA duplexes and generate force to condense DNA through long-range interactions. These findings provide insight into the conserved networks of protein-protein and protein-DNA interactions that promote condensate formation and meiotic DSBs.
GENES & DEVELOPMENT
(2023)
Article
Cell Biology
Xiaojing Mu, Hajime Murakami, Neeman Mohibullah, Scott Keeney
GENES & DEVELOPMENT
(2020)