Article
Multidisciplinary Sciences
Sreesankar Easwaran, Matthew Van Ligten, Mackenzie Kui, Denise J. Montell
Summary: This study reveals that Drosophila enter adult reproductive diapause under specific environmental conditions, which leads to ovarian arrest but preserves fertility. Germline stem cells (GSCs) in diapause incur DNA damage and division reduction, yet they are able to recover. Mimicking reduced juvenile hormone production during diapause enhances GSC longevity in non-diapausing flies.
NATURE COMMUNICATIONS
(2022)
Article
Behavioral Sciences
Janani Iyer, Siddhita D. Mhatre, Rachel Gilbert, Sharmila Bhattacharya
Summary: The review discusses the advancements in gravitational biology using fruit flies as a spaceflight model organism, providing significant information on neuro-behavioral, aging, immune, cardiovascular, developmental, and multi-omics changes.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Elisabetta Catalani, Agnese Cherubini, Simona Del Quondam, Davide Cervia
Summary: Understanding the condition of the retina in neurodegenerative diseases is crucial for therapeutic development. Zebrafish and fruit flies offer promising advantages as alternative models for studying neurodegenerative diseases and retinal pathologies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Viktor Vedelek, Attila L. Kovacs, Gabor Juhasz, Elham Alzyoud, Rita Sinka
Summary: In this study, researchers discovered a previously unknown tissue-specific role of the Drosophila archipelago (ago) gene in spermatid differentiation, affecting spermatid development and mitochondrial morphology. Silencing ago gene confirmed spermatogenesis defects. Mutants of ago gene in Drosophila exhibit abnormalities in spermatids, including cyst morphology, mitochondrial structures, and individualization defects.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Martyna Gajos, Olga Jasnovidova, Alena van Boemmel, Susanne Freier, Martin Vingron, Andreas Mayer
Summary: Research reveals widespread RNA polymerase pausing in human cells, mostly occurring along the gene-body of transcribed genes rather than in promoter-proximal regions. Machine learning modeling identifies DNA sequence properties underlying transcriptional pausing, suggesting potential functional roles of exact pause locations in gene expression.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
David W. J. McQuarrie, Adam M. Read, Frannie H. S. Stephens, Alberto Civetta, Matthias Soller
Summary: Nuclear pore proteins (Nups) have been identified as genes involved in speciation from hybrid incompatibility in Drosophila. Positive selection has been observed in the evolution of Nup96 and Nup160 coding sequences, suggesting their role in nucleoporin evolution. The functionality of channel protein Nup54 is crucial for the female post-mating response, and rapid evolution in its core promoter region indicates the importance of transcriptional regulatory elements in speciation. Rapid accumulation of insertions/deletions (indels) is also observed in the promoters of Nup58 and Nup62, suggesting an evolutionary mechanism driven by indel accumulation in core Nup promoters.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Wiem Ben Amara, Hadi Quesneville, Maha Mezghani Khemakhem
Summary: The availability of the whole-genome sequence of the wheat pest Mayetiola destructor allowed for investigation into the content and relationship of Transposable Elements (TEs) with genes involved in insect virulence. Analysis revealed that TEs make up approximately 16% of the genome, with a majority being inactive due to accumulated deletions. Two bursts of TE activity were detected at 20% and 2% divergence, involving different TE families and suggesting potential new TE invasions.
Article
Genetics & Heredity
Sergio Casas-Tinto, Alberto Ferrus
Summary: The study found that haplolethals associated with the gene wupA result from the combined insufficiency of a large number of Troponin I isoforms. These findings reveal novel aspects of gene expression and may have implications for evolutionary gene splitting.
Article
Biotechnology & Applied Microbiology
Ya Zheng, Bin Mao, Qian Wang, Xin Duan, Meng-Yan Chen, Wei Shen, Chao Li, Yu-Feng Wang
Summary: Knockdown of ocn gene in Drosophila testes resulted in smaller testis without germ cells. Through proteomics sequencing, 606 proteins were identified as significantly changed in expression after ocn knockdown. The down-regulation of ocn disturbed key signaling pathways related to cell survival and differentiation.
Article
Multidisciplinary Sciences
Anil K. Panigrahi, David M. Lonard, Bert W. O'Malley
Summary: This study demonstrates the interdependence of transcription between enhancers and target promoters. The results suggest that transcriptional concurrence and coordination throughout the genome are based on the transcriptional interdependence of enhancers and promoters. The study proposes a model where enhancers and promoters are entangled in the form of enhancer-promoter contact, reside in a proteinaceous bubble, and utilize shared transcriptional resources and regulatory inputs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Lily Li, Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: The study reveals that the expression of developmental genes is regulated by multiple enhancers and core promoters, which provide both redundancy and specificity. Specific burst properties during transcription, such as burst size and frequency, are most strongly tuned by the combination of promoters and enhancers. The presence of multiple promoters in a locus is due to enhancer preference and a need for redundancy, with broad promoters being common among developmental genes.
Article
Chemistry, Medicinal
Letizia Pruccoli, Carlo Breda, Gabriella Teti, Mirella Falconi, Flaviano Giorgini, Andrea Tarozzi
Summary: The study found that esculetin (ESC) can partially inhibit neuronal death caused by mHTT, counteract oxidative stress and mitochondrial impairment, and reduce the progression of Huntington's disease. ESC also showed the ability to counteract neuronal death in a Drosophila model and had a positive impact on the HD phenotype.
Article
Cell Biology
Xi Liu, Peter Nagy, Alessandro Bonfini, Philip Houtz, Xiao-Li Bing, Xiaowei Yang, Nicolas Buchon
Summary: Gut microbes play an important role in the differentiation of gut stem cells, influencing epithelial composition and gut physiology. The balance between microbial pattern recognition pathways and damage response pathways is crucial for stem cell differentiation.
Article
Biochemistry & Molecular Biology
Amanda K. Chaplin, Steven W. Hardwick, Antonia Kefala Stavridi, Christopher J. Buehl, Noah J. Goff, Virginie Ropars, Shikang Liang, Taiana Maia De Oliveira, Dimitri Y. Chirgadze, Katheryn Meek, Jean-Baptiste Charbonnier, Tom L. Blundell
Summary: Non-homologous end joining (NHEJ) is a critical mechanism for repairing DNA double-strand breaks in humans, involving core proteins such as Ku70/80 heterodimer. Cryo-EM structures of NHEJ supercomplexes reveal detailed structural assembly and mutational disruption of these complexes negatively affects DNA repair.
Article
Biology
Xueying C. Li, Timothy Fuqua, Maria Elize van Breugel, Justin Crocker
Summary: Rapid enhancer and slow promoter evolution have been demonstrated through comparative genomics. However, it is not clear how this information is encoded genetically and if this can be used to place evolution in a predictive context. Here, researchers investigated the evolutionary capacity of promoter variation in Drosophila melanogaster through an unbiased mutation library survey. They found that mutations in promoters had limited to no effect on spatial patterns of gene expression. Compared to developmental enhancers, promoters are more robust to mutations and have more access to mutations that can increase gene expression, suggesting that their low activity might be a result of natural selection.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ann Boija, Dig Bijay Mahat, Aman Zare, Per-Henrik Holmqvist, Philge Philip, David J. Meyers, Philip A. Cole, John T. Lis, Per Stenberg, Mattias Mannervik
Article
Biochemistry & Molecular Biology
Hila Sameach, Aya Narunsky, Salome Azoulay-Ginsburg, Lada Gevorkyan-Aiapetov, Yonathan Zehavi, Yoni Moskovitz, Tamar Juven-Gershon, Nir Ben-Tal, Sharon Ruthstein
Article
Genetics & Heredity
Dustin Shigaki, Orit Adato, Aashish N. Adhikari, Shengcheng Dong, Alex Hawkins-Hooker, Fumitaka Inoue, Tamar Juven-Gershon, Henry Kenlay, Beth Martin, Ayoti Patra, Dmitry D. Penzar, Max Schubach, Chenling Xiong, Zhongxia Yan, Alan P. Boyle, Anat Kreimer, Ivan Kulakoyskiy, John Reid, Ron Unger, Nir Yosef, Jay Shendure, Nadav Ahituv, Martin Kirche, Michael A. Beer
Article
Multidisciplinary Sciences
Hila Shir-Shapira, Anna Sloutskin, Orit Adato, Avital Ovadia-Shochat, Diana Ideses, Yonathan Zehavi, George Kassavetis, James T. Kadonaga, Ron Unger, Tamar Juven-Gershon
Article
Multidisciplinary Sciences
Suresh Sajwan, Mattias Mannervik
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Roshan Vaid, Jiayu Wen, Mattias Mannervik
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemical Research Methods
Tgst Levi, Anna Sloutskin, Rachel Kalifa, Tamar Juven-Gershon, Offer Gerlitz
BIOLOGICAL PROCEDURES ONLINE
(2020)
Article
Oncology
Orit Adato, Yaron Orenstein, Juri Kopolovic, Tamar Juven-Gershon, Ron Unger
Article
Biochemistry & Molecular Biology
Isabel Regadas, Olle Dahlberg, Roshan Vaid, Oanh Ho, Sergey Belikov, Gunjan Dixit, Sebastian Deindl, Jiayu Wen, Mattias Mannervik
Summary: The study identified a unique chromatin state with histone 3 lysine 14 acetylation in key tissue-specific genes in Drosophila and human cells. Functional experiments demonstrated that H3K14 is essential for the expression of genes lacking canonical histone modifications, highlighting its crucial role in tissue-specific gene regulation.
Article
Biochemical Research Methods
Rene Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon
Summary: This study identified preferred downstream positions in human promoters resembling the fruit fly DPE, supporting the presence of Inr+DPE-containing promoters in human genes. Functional characterization of these positions also suggests a spacing dependency on the Inr, indicating the likelihood of common canonical Inr+DPE promoters in metazoan species.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Cell Biology
Anna Sloutskin, Hila Shir-Shapira, Richard N. Freiman, Tamar Juven-Gershon
Summary: The core promoter region is an active regulatory module in transcriptional programs, controlling developmental genes through downstream regions like the DPE. Promoter-dependent basal transcription machinery emphasizes the importance of specialized transcription complexes in driving embryonic development and morphogenesis. Enhancer specificity and transcription burst size are regulated by the core promoter content, highlighting its importance in developmental gene expression networks.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Sun Y. Maybury-Lewis, Abigail K. Brown, Mitchell Yeary, Anna Sloutskin, Shleshma Dhakal, Tamar Juven-Gershon, Ashley E. Webb
Summary: The study identified chromatin accessibility differences in neural stem/progenitor cells in quiescent and activated states, revealing unique and shared chromatin profiles associated with gene regulation. Active enhancers bound by pro-neurogenic and quiescence factors were specific to activation or quiescence, while shared sites were enriched for elements related to translation and metabolism. Furthermore, the research discovered a novel mechanism where many sites linked to gene repression become accessible during NSC activation, and how age-related changes affect chromatin regions associated with metabolic and transcriptional functions in aged NSCs.
Article
Chemistry, Multidisciplinary
Shira Roth, Diana Ideses, Tamar Juven-Gershon, Amos Danielle
Summary: Identifying and investigating protein-DNA interactions is crucial for biological research. The magnetic modulation biosensing (MMB) system offers a simple and efficient alternative method for detecting these interactions, with faster turnaround times and more accurate results compared to current techniques.
Article
Biochemistry & Molecular Biology
George Hunt, Ann Boija, Mattias Mannervik
Summary: Maintenance of appropriate cell states involves epigenetic mechanisms, including Polycomb-group (PcG)-mediated transcriptional repression. This study reveals the association between the p300/CREB-binding protein (CBP) co-activator and PcG regions in Drosophila and mouse cells. CBP stabilizes Pol II at PcG-bound repressive sites and promotes Pol II pausing, which are necessary for R-loop formation and nucleosome depletion at Polycomb Response Elements (PREs), thereby supporting PcG-mediated silencing.
Article
Oncology
Alexander Pfab, Sergey Belikov, Michaela Keuper, Martin Jastroch, Mattias Mannervik
Summary: This study found that the neurotoxin symbolscript can trigger cell death of dopamine neurons, leading to Parkinson's disease symptoms. Additionally, the neurotoxin directly affects mitochondrial function and transcription, resulting in reduced ATP production. These findings reveal the direct effects of symbolscript on cellular processes, while other gene expression or epigenetic changes are secondary effects reflecting cellular adaptation.
EXPERIMENTAL CELL RESEARCH
(2023)