Article
Cell Biology
Li-Sheng Zhang, Qing-Ping Xiong, Sonia Pena Perez, Chang Liu, Jiangbo Wei, Cassy Le, Linda Zhang, Bryan T. Harada, Qing Dai, Xinran Feng, Ziyang Hao, Yuru Wang, Xueyang Dong, Lulu Hu, En-Duo Wang, Tao Pan, Arne Klungland, Ru-Juan Liu, Chuan He
Summary: ALKBH7 is identified as an RNA demethylase that controls nascent mitochondrial RNA processing and mitochondrial activity, with depletion leading to increased processing of polycistronic mitochondrial RNA, reduced levels of mitochondria-encoded tRNA and protein translation, as well as decreased mitochondrial activity.
NATURE CELL BIOLOGY
(2021)
Article
Immunology
Atila Duque Rossi, Luiza Mendonca Higa, Alice Laschuk Herlinger, Marcelo Ribeiro-Alves, Mariane Talon de Menezes, Ana Lucia Moraes Giannini, Cynthia Chester Cardoso, Andrea T. T. Da Poian, Amilcar Tanuri, Renato Santana Aguiar
Summary: An analysis of the expression levels of 754 human microRNAs in DENV-infected THP-1 cells revealed differential expression of 11 human microRNAs, with gene ontology and enrichment analysis highlighting potential biological processes affected by these molecules.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Yan Liu, Zihan Wu, Damu Wu, Ning Gao, Jinzhong Lin
Summary: A Ribozyme-Assisted Polycistronic co-expression system (pRAP) was developed for heterologous co-production and in vivo assembly of multi-subunit complexes. The system allows balanced expression of subunits, allowing faithful protein complex assembly. Successful reconstitution of large functional multi-subunit complexes validates the utility of pRAP for studying biological processes.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pellegrino, Sophie-Charlotte Fabig, Dilara Kersebaum, Philipp Huellemann, Ralf Baron, Toralf Roch, Nina Babel, Harald Seitz
Summary: This study identified four microRNAs that may be linked to degenerative processes, blood flow regulation, and signal transduction, potentially leading to chronic painful PNP. These microRNAs may serve as potential novel biomarkers and have therapeutic implications.
Article
Biochemistry & Molecular Biology
Luigi Mansi, Marco Antonio Tangaro, Claudio Lo Giudice, Tiziano Flati, Eli Kopel, Amos Avraham Schaffer, Tiziana Castrignano, Giovanni Chillemi, Graziano Pesole, Ernesto Picardi
Summary: RNA editing is a significant epitranscriptome phenomenon that enhances the diversity of eukaryotic organisms, particularly in humans. While playing crucial roles in gene expression regulation, innate immune response modulation, and neurotransmitter receptor functioning, there is still a need for further research to uncover unknown aspects of RNA editing biology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Elizabeth A. Brija, Zhuo Guan, Suresh K. Jetti, Troy Littleton
Summary: This study demonstrates that RNA editing of the C-terminus of Cpx modifies its control ability for SNARE-mediated fusion and alters presynaptic output. The RNA editing of Cpx in single neurons is random and can fine tune neurotransmitter release by altering subcellular localization and clamping properties of the protein.
Article
Biochemistry & Molecular Biology
Veronika Altmannova, Andreas Blaha, Susanne Astrinidis, Heidi Reichle, John R. Weir
Summary: The choice of expression organism is critical for successful production of recombinant proteins, with Escherichia coli and baculovirus/insect cell expression system being the most commonly used for structural studies. An integrated system allowing simultaneous cloning into both E. coli and baculovirus expression vectors can enhance experimental efficiency and flexibility.
Article
Cell Biology
Ziyue Mi, Li Gong, Yujie Kong, Peizhe Zhao, Yonghua Yin, Haixia Xu, Li Tian, Zhong Liu
Summary: This study examines the expression profiles of exosomal microRNAs in apheresis platelet concentrates during storage and predicts the potential functions of target genes. The results show that differentially expressed microRNAs are involved in positive regulation of cell proliferation and nervous system development. They are mainly enriched in signaling pathways related to the regulation of pluripotency of stem cells, prolactin, and FoxO. Understanding the role of exosomal microRNAs in platelet transfusion can help improve the safety and efficacy of this clinical treatment.
Article
Neurosciences
Ali Jason Saleh, Hans Gerd Nothwang
Summary: A comparative study of miRNA expression during development of the auditory hindbrain in mammals and chickens revealed both shared and distinct features. In the nucleus magnocellularis, differential expression patterns along the cochleotopic axis were observed, with miRNAs reflecting different rhombomeric origins. Bioinformatics analysis predicted mRNA targets associated with neuronal developmental processes. Overall, this study adds miRNA patterns to the list of cochleotopic and developmental gradients in the central auditory system.
JOURNAL OF COMPARATIVE NEUROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sarah Janati-Idrissi, Mariana Roza de Abreu, Cervin Guyomar, Fernanda de Mello, Thaovi Nguyen, Nazim Mechkouri, Stephanie Gay, Jerome Montfort, Anne Alicia Gonzalez, Marzieh Abbasi, Jerome Bugeon, Violette Thermes, Herve Seitz, Julien Bobe
Summary: This study provides a proof of concept for the successful identification of miRNA phenotypic targets from RNA-seq data. The researchers identified tead3b as a target of miR-202-5p, which is involved in ovarian function and egg production. This study highlights the importance of understanding miRNA functions and their targets in order to better understand biological processes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Sung Cheon Ko, Han Min Woo
Summary: This study reports a method for bacterial RNA repression using the CRISPR-dCas13a system. By using programmable crRNAs, trans-acting and cis-acting sRNAs can be repressed, altering the regulatory mechanisms and stress-related phenotypes in bacteria. This system can be used for discovering novel sRNAs and fine-tuning bacterial RNA repression in both scientific and industrial applications.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Oncology
Gioacchino P. Marceca, Luisa Tomasello, Rosario Distefano, Mario Acunzo, Carlo M. Croce, Giovanni Nigita
Summary: A-to-I editing in RNA plays a crucial role in cancer biology, affecting miRNA function with clinical significance. Challenges remain in identifying and characterizing miRNA editing events in tumors.
Article
Chemistry, Multidisciplinary
Kaixin Lyu, Shuo-Bin Chen, Eugene Yui-Ching Chow, Haizhou Zhao, Jia-Hao Yuan, Meng Cai, Jiahai Shi, Ting-Fung Chan, Jia-Heng Tan, Chun Kit Kwok
Summary: RNA G-quadruplex (rG4) structure in the 5' untranslated region (5' UTR) of ADAR1 mRNA has been identified and characterized. This structure functions as an inhibitory element in translation and interacts with the helicase DHX36 to modulate translation. These findings illustrate the significance of the rG4 structure in controlling ADAR1 translation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Sang Eun Park, Wonju Kim, Ji-Ye Hong, Dayeon Kang, Seulki Park, Jungyo Suh, Dalsan You, Yun-Yong Park, Nayoung Suh, Jung Jin Hwang, Choung-Soo Kim
Summary: This study identified miR-96-5p as a key regulator in sunitinib resistance in CCRCC by direct suppression of PTEN, leading to poor prognosis in patients with high miR-96-5p and low PTEN levels.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Hang Jie, Zhongxian Xu, Jian Gao, Feng Li, Yinglian Chen, Dejun Zeng, Guijun Zhao, Diyan Li
Summary: In this study, Illumina deep sequencing technology was used to analyze the small RNA transcriptome of unmated and mated male Chinese forest musk deer, revealing 1,652 known miRNAs and 45 novel miRNAs with differential expression. Target gene functional enrichment in unmated males showed more involvement in structural molecule activity and cellular exocytosis processes, suggesting a potential role of these genes in musk formation. Further investigation into specific miRNA-mRNA pairs may shed light on the development and secretion of musk gland in this species.
Article
Genetics & Heredity
Yen-Chi Wu, Geetanjali Chawla, Nicholas Sokol
G3-GENES GENOMES GENETICS
(2020)
Article
Biology
Simranjot Bawa, David S. Brooks, Kathryn E. Neville, Marla Tipping, Md Abdul Sagar, Joseph A. Kollhoff, Geetanjali Chawla, Brian Geisbrecht, Jason M. Tennessen, Kevin W. Eliceiri, Erika R. Geisbrecht
Editorial Material
Biochemistry & Molecular Biology
Nicholas S. Sokol, Irene L. G. Newton
TRENDS IN MICROBIOLOGY
(2020)
Article
Genetics & Heredity
Danny E. Miller, Lily Kahsai, Kasun Buddika, Michael J. Dixon, Bernard Y. Kim, Brian R. Calvi, Nicholas S. Sokol, R. Scott Hawley, Kevin R. Cook
G3-GENES GENOMES GENETICS
(2020)
Article
Developmental Biology
Kasun Buddika, Jingjing Xu, Ishara S. Ariyapala, Nicholas S. Sokol
Summary: The research introduces a proximity-based RNA analysis method using a GAL4 driver strategy exclusively expressed in intestinal progenitor cells in Drosophila. This method allows for the identification of the majority of transcripts found after progenitor cell sorting with low background noise from whole animal lysate. Additionally, the study reveals the binding motif of Fragile X mental retardation protein (FMRP) in Drosophila cells for the first time using enhanced crosslinking and immunoprecipitation (eCLIP).
Review
Biochemistry & Molecular Biology
Manish Pandey, Divya Ojha, Sakshi Bansal, Ambadas B. Rode, Geetanjali Chawla
Summary: The versatility of RNAs makes them ideal for overcoming the limitations of small molecule-based drugs in biopharmaceuticals. RNA-based therapeutics face challenges such as instability, delivery to diseased cells, and immunogenicity. Recent advancements in delivery systems and chemical modifications have facilitated the entry of exogenous RNAs into clinical trials for treating infectious diseases.
MOLECULAR ASPECTS OF MEDICINE
(2021)
Article
Biology
Manish Pandey, Sakshi Bansal, Sudipta Bar, Amit Kumar Yadav, Nicholas S. Sokol, Jason M. Tennessen, Pankaj Kapahi, Geetanjali Chawla
Summary: In fruit flies, two neuronally enriched and highly conserved microRNAs, miR-125 and let-7, have been shown to mediate the response to dietary restriction (DR) that extends lifespan. MiR-125 functions in neurons, while its target gene chinmo modulates fat metabolism and longevity in both neurons and the fat body. Chinmo exerts its DR effects by regulating the expression of several proteins, indicating a potential avenue for miR-125 and its downstream effectors as drug candidates for late-onset diseases and biomarkers for healthy aging in humans.
Review
Cell Biology
Kenneth A. Wilson, Manish Chamoli, Tyler A. Hilsabeck, Manish Pandey, Sakshi Bansal, Geetanjali Chawla, Pankaj Kapahi
Summary: Dietary restriction is considered a robust means to extend lifespan and healthspan, but its effects often vary among individuals and tissues. Many aging-associated mechanisms are nutrient responsive, yet the potential of lifespan interventions like DR to extend healthspan is commonly overlooked in aging studies.
Article
Biochemistry & Molecular Biology
Kasun Buddika, Yi-Ting Huang, Ishara S. Ariyapala, Alex Butrum-Griffith, Sam A. Norrell, Alex M. O'Connor, Viraj K. Patel, Samuel A. Rector, Mark Slovan, Mallory Sokolowski, Yasuko Kato, Akira Nakamura, Nicholas S. Sokol
Summary: The study reveals that adult Drosophila intestinal stem cells contain P-bodies, and loss of P-bodies leads to the loss of stem cells and inappropriate expression of differentiation genes. Transcriptomic analysis identifies a P-body-dependent repression activity that coordinates with known transcriptional repression programs to maintain stem cells in a state primed for differentiation.
Article
Geriatrics & Gerontology
Manish Pandey, Sakshi Bansal, Geetanjali Chawla
Summary: This study found that biofortified blue wheat can prolong the lifespan of fruit flies and modulate gene expression. Supplementation with blue or purple wheat provides better protection against oxidative stress and prevents lifespan reduction and cardiac pathologies associated with high-fat diet intake.
EXPERIMENTAL GERONTOLOGY
(2022)
Article
Genetics & Heredity
Ishara S. Ariyapala, Kasun Buddika, Heather A. Hundley, Brian R. Calvi, Nicholas S. Sokol
Summary: This study reveals the critical role of the nuclear RNA-binding protein Swm in the maintenance of Drosophila intestinal stem cells and their daughter cells. Loss of Swm leads to cell detachment and severe loss of progenitor cells. Swm is involved in post-transcriptional regulation of mRNAs encoding cell adhesion proteins.
Article
Cell Biology
Manish Pandey, Arthur Luhur, Nicholas S. S. Sokol, Geetanjali Chawla
Summary: This study investigated the impact of position, order, stem-base, and terminal loop sequences on the differential processing of miRNAs in clustered microRNAs. The results highlighted the importance of structural attributes in regulating the expression of polycistronic miRNAs and provided specific guidelines for achieving differential expression within a cluster.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Sromana Mukherjee, Brian R. Calvi, Heather A. Hundley, Nicholas S. Sokol
Summary: MicroRNA miR-956 controls the commitment to the terminally differentiated enterocyte cell fate in the Drosophila intestine, specifically regulating Notch signaling activity in intermediate enteroblast progenitor cells. MiR-956 targets insensitive mRNA to regulate EB/EC ratios by repressing Notch activity in EBs. Overall, our study highlights a post-transcriptional gene-regulatory mechanism for controlling differentiation in an adult intestinal stem cell lineage.
Article
Biochemical Research Methods
Manish Pandey, Geetanjali Chawla
Summary: The protocol described focuses on the optimized isolation and characterization of exosomes from a Drosophila melanogaster cell line, with a specific emphasis on examining protein loading in starvation-induced exosomes.