Article
Genetics & Heredity
Jiaqi Li, Jingjing Wang, Peijing Zhang, Renying Wang, Yuqing Mei, Zhongyi Sun, Lijiang Fei, Mengmeng Jiang, Lifeng Ma, E. Weigao, Haide Chen, Xinru Wang, Yuting Fu, Hanyu Wu, Daiyuan Liu, Xueyi Wang, Jingyu Li, Qile Guo, Yuan Liao, Chengxuan Yu, Danmei Jia, Jian Wu, Shibo He, Huanju Liu, Jun Ma, Kai Lei, Jiming Chen, Xiaoping Han, Guoji Guo
Summary: This study generated single-cell whole-body expression landscapes of zebrafish, Drosophila, and earthworm using Microwell-seq. By integrating cell landscapes from eight representative species, the researchers developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory programs. Conserved genetic regulation in vertebrates and invertebrates were revealed through comparison of cell-type-specific transcription factors. This work provides a valuable resource and a new strategy for studying regulatory grammar in diverse biological systems.
Article
Multidisciplinary Sciences
Lili Zhou, Caitlyn Miller, Loren J. Miraglia, Angelica Romero, Ludovic S. Mure, Satchidananda Panda, Steve A. Kay
Summary: This study identified the miRNA cluster miR-183/96/182 as key regulators of circadian rhythms, with miR-96 directly targeting the core circadian clock gene PER2. Knockout of the miR-183/96/182 cluster in mice showed tissue-specific effects on circadian parameters, highlighting the importance of miRNAs as a genome-wide layer of circadian clock regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
John E. La Marca, Brandon J. Aubrey, Bruce Yang, Catherine Chang, Zilu Wang, Andrew Kueh, Lin Tai, Stephen Wilcox, Liz Milla, Susanne Heinzel, David Vremec, Lauren Whelan, Christina Konig, Deeksha Kaloni, Anne K. Voss, Andreas Strasser, Sarah T. Diepstraten, Marco J. Herold, Gemma L. Kelly
Summary: Whole-genome screens using CRISPR technologies can identify novel tumour suppressors and factors affecting cancer cell response to anti-cancer drugs. In this study, a genome-wide screen on lymphoma cells found that the absence of ARRDC3 enhances the survival and competitiveness of MYC-driven lymphoma cells treated with TRP53-activating anti-cancer drugs. Deleting Arrdc3 in mice resulted in perinatal lethality and cardiac defects. The absence of ARRDC3 significantly accelerated MYC-driven lymphoma development, highlighting its role as a new mediator of TRP53-mediated tumour suppression.
CELL DEATH AND DIFFERENTIATION
(2023)
Review
Cell Biology
Antonio Baonza, Sara Tur-Gracia, Marina Perez-Aguilera, Carlos Estella
Summary: Cells have evolved mechanisms to respond to DNA damage and maintain genomic integrity. The responses include cell cycle checkpoints, repair mechanisms, and induction of apoptosis. Understanding the coordination between cell proliferation control and apoptosis is crucial for tissue homeostasis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Olga V. Andreenkova, Olga D. Shishkina, Alexandra I. Klimenko, Aleksandra E. Korenskaia, Margarita A. Bobrovskikh, Natalja V. Shatskaya, Gennady V. Vasiliev, Nataly E. Gruntenko
Summary: Several methods for extracting Wolbachia DNA from insect hosts have been described, but the low quantity of the bacteria made these techniques labor-intensive. This paper proposes a simplified and accelerated method for isolating high-purity Wolbachia DNA from Drosophila melanogaster, using centrifugation, filtration, and a modified version of the Livak buffer protocol. The proportion of Wolbachia DNA in total DNA was quantified using sequencing and bioinformatic analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jeroen Dobbelaere, Tiffany Y. Su, Balazs Erdi, Alexander Schleiffer, Alexander Dammermann
Summary: Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. In this study, a set of 386 human genes associated with cilium assembly or motility were identified by analyzing the presence and absence pattern in the genomes of diverse eukaryotes. The novel genes were further characterized and found to be related to cilium defects in fruit flies and nematodes. This dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and provides a valuable resource for future studies.
Article
Biochemistry & Molecular Biology
Ekaterina Proshkina, Elena Yushkova, Liubov Koval, Nadezhda Zemskaya, Evgeniya Shchegoleva, Ilya Solovev, Daria Yakovleva, Natalya Pakshina, Natalia Ulyasheva, Mikhail Shaposhnikov, Alexey Moskalev
Summary: Small RNAs play a crucial role in coordinating various cellular processes, affecting gene expression, genomic stability, and suppressing mutagenic transposon activity, thus influencing aging, longevity, and sensitivity to stress factors. Proteins of the Argonaute family are essential for the biogenesis and activity of small RNAs, but their role in regulating lifespan and radioresistance is still not well understood. Studies on knockdown of Argonaute genes in different tissues of Drosophila melanogaster show tissue-specific effects on lifespan, survival after irradiation, and retrotransposon levels, providing insights into the associated molecular mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Hematology
Chuang Jiang, Maoxiang Qian, Yoshihiro Gocho, Wentao Yang, Guoqing Du, Shuhong Shen, Jun J. Yang, Hui Zhang
Summary: Epigenetic alterations, such as histone acetylation, play a significant role in the malignant transformation of hematopoietic cells and the progression of diseases. Panobinostat, a pan-histone deacetylase inhibitor, has been approved for the treatment of multiple myeloma and shows promise in treating acute lymphoblastic leukemia (ALL). However, the mechanism of drug resistance in ALL is still largely unknown. Through genome-wide screening, researchers identified mitochondrial activity as the driver of panobinostat resistance in ALL. They discovered that the ectopic expression of SIRT1 activated mitochondrial activity and sensitized ALL to panobinostat treatment by activating the mitochondria-related apoptosis pathway. The transcription level of SIRT1 was also found to be significantly associated with panobinostat sensitivity in different types of tumors, suggesting it could be a potential biomarker for panobinostat response in cancers. The study suggests that patients with higher SIRT1 expression in cancer cells may benefit from panobinostat treatment, and combination therapy with SIRT1 or mitochondrial activators could overcome panobinostat resistance.
Article
Cell Biology
Dong Li, Ying Ge, Ze Zhao, Rui Zhu, Xiang Wang, Xiaolin Bi
Summary: The study analyzed the expression profiles of miRNAs and piRNAs in Drosophila during development and DNA damage response, revealing dynamic expression patterns and the key roles of E2f1 and p53 in regulating small ncRNAs. E2f1 may play a major role in modulating miRNAs during development and after X-ray irradiation, showcasing new insights into small ncRNA biology.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Medicine, Research & Experimental
Silvia Alemany, Maria Soler-Artigas, Judit Cabana-Dominguez, Dana Fakhreddine, Natalia Llonga, Laura Vilar-Ribo, Amanda Rodriguez-Urrutia, Judit Palacio, Ana Maria Gonzalez-Castro, Beatriz Lobo, Carmen Alonso-Cotoner, Magnus Simren, Javier Santos, Josep Antoni Ramos-Quiroga, Marta Ribases
Summary: In this study, a multi-trait genome-wide association study was conducted to explore the genetic overlap between irritable bowel syndrome (IBS), neuroticism, depression, and anxiety. The results revealed a polygenic architecture for IBS and identified novel genetic variants associated with the disorder. The analysis also showed bidirectional causal effects between IBS and neuroticism and depression, as well as the genetic liability of IBS on anxiety. These findings contribute to our understanding of the genetic basis and relationships between gastrointestinal and mental disorders.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Ronald D. Smith, Joshua R. Puzey, Gregory D. Conradi Smith
Summary: In an empirical analysis, it was found that transposable element count in natural populations of Mimulus guttatus and Drosophila melanogaster showed a surprisingly high variance. This variance is likely due to copy-and-paste proliferation dynamics rather than purifying selection on total element load.
Article
Biology
Ananya Chakravarti, Heshani N. Thirimanne, Savanna Brown, Brian R. Calvi
Summary: Using Drosophila as a model, this study found that p53 isoforms in fruit flies have functions specific to DNA damage and cell types, similar to mammalian p53 family members in the genotoxic stress response and oocyte quality control.
Article
Hematology
Takashi Ishio, Sarvesh Kumar, Joji Shimono, Anusara Daenthanasanmak, Sigrid Dubois, Yuquan Lin, Bonita Bryant, Michael N. Petrus, Emmanuel Bachy, Da Wei Huang, Yandan Yang, Patrick L. Green, Hiroo Hasegawa, Michiyuki Maeda, Hideki Goto, Tomoyuki Endo, Takashi Yokota, Kanako C. Hatanaka, Yutaka Hatanaka, Shinya Tanaka, Yoshihiro Matsuno, Yibin Yang, Satoshi Hashino, Takanori Teshima, Thomas A. Waldmann, Louis M. Staudt, Masao Nakagawa
Summary: The study identifies CDK6 as a novel therapeutic target for adult T-cell leukemia/lymphoma (ATLL) and suggests the potential of combining CDK6 inhibitor palbociclib with mTORC1 inhibitors for treating this difficult malignancy.
Article
Biology
Deeptiman Chatterjee, Caique Almeida Machado Costa, Xian-Feng Wang, Allison Jevitt, Yi-Chun Huang, Wu-Min Deng
Summary: This study reveals the mechanisms underlying the effect of polarity loss on cell plasticity through single cell RNA sequencing. The study of Drosophila ovaries reveals the link between Keap1-Nrf2 signaling and cell plasticity in early tumorigenesis.
Article
Biochemistry & Molecular Biology
Alexandru Al Ecovoiu, Alexandru Marian Bologa, David Ioan Mihail Chifiriuc, Andrei Mihai Ciuca, Nicoleta Denisa Constantin, Iulian Constantin Ghionoiu, Iulian Cristian Ghita, Attila Cristian Ratiu
Summary: This study presents the new functions of GA_v2 tool for mapping and annotation of transposons and demonstrates its applicability in the genome of D. melanogaster. The results indicate that GA_v2 is a reliable and autonomous tool for transposon mapping and annotation in genomes sequenced by long sequencing technology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)