Review
Biochemistry & Molecular Biology
Ryo Onishi, Soichiro Yamanaka, Mikiko C. Siomi
Summary: The piRNA pathway is a self-defense mechanism essential for maintaining germline genome integrity, suppressing transposons through RNA degradation and heterochromatinization. While showing conservation across species, there is clear biodiversity in the overall schemes of nuclear events.
Review
Plant Sciences
Jayanti Jodder
Summary: miRNAs in plants play a crucial role in controlling growth, development, and stress tolerance by modulating the expression of target genes. Modulating the expression of specific stress/development-related genes can be achieved by targeting the corresponding miRNAs. Understanding the molecular mechanism of miRNA biogenesis, particularly the processing of pri-MIRNAs, is essential for effectively modulating miRNA expression levels and ultimately improving plant yield and stress tolerance.
PLANT CELL REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Anup S. Pathania, Philip Prathipati, Kishore B. Challagundla
Summary: Recent advances in extracellular vesicle biology have highlighted the critical role of these vesicles in maintaining cell homeostasis and immune surveillance, particularly in the context of cancer research. Exosomes can influence cell communication by transferring biomolecules, impacting immune cell responses within the tumor microenvironment.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2021)
Article
Multidisciplinary Sciences
Arnab Das, Sudarshana Basu, Diptankar Bandyopadhyay, Kamalika Mukherjee, Debduti Datta, Sreemoyee Chakraborty, Sayantan Jana, Moumita Adak, Sarpita Bose, Saikat Chakrabarti, Snehasikta Swarnakar, Partha Chakrabarti, Suvendra N. Bhattacharyya
Summary: miR-122 in the mammalian liver regulates metabolic homeostasis and plays a role in controlling tissue inflammation through intercellular transfer. MMP2 is essential for the transfer of extracellular vesicles and their miRNA content between hepatic and non-hepatic cells.
Article
Chemistry, Applied
Pierre-Olivier Bussiere, Jean-Luc Gardette, Geraldine Rapp, Claire Masson, Sandrine Therias
Summary: Chitosan films were subjected to accelerated artificial weathering in the presence of oxygen, resulting in changes in chemical structure, formation of gluconolactone derivatives, detection of low molecular weight photoproducts, occurrence of crosslinking reactions, and variations in mechanical and surface properties. These changes were observed and correlated at molecular scale, showing a reduction in macroscopic properties.
CARBOHYDRATE POLYMERS
(2021)
Review
Endocrinology & Metabolism
Mirjana Macvanin, Zoran Gluvic, Jelena Radovanovic, Magbubah Essack, Xin Gao, Esma R. Isenovic
Summary: Cardiovascular disorders are increasingly common and pose a significant global health issue. Recent research emphasizes the importance of insulin-like growth factor 1 (IGF-1) in maintaining cardiovascular health.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Environmental Sciences
Boqiong Wu, Renhe Jiao, Dongyao Cui, Tanjun Zhao, Jian Song, Yaoyao Zhan, Yaqing Chang
Summary: Comparative miRNA and mRNA transcriptome analyses of sea urchins with different gonadal colors revealed genes and miRNAs associated with sex and gonadal coloration. These findings are important for understanding the process of sea urchin gonad coloration and improving the quality of sea urchins.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Sanjay Dey, Claire Batisse, Jinal Shukla, Michael W. Webster, Maria Takacs, Charlotte Saint-Andre, Albert Weixlbaumer
Summary: This article investigates the regulatory mechanism of RNA in its own synthesis. Cryo-EM reconstructions reveal that U-rich RNA sequences can promote widening of the RNAP nucleic-acid-binding channel, facilitating transcript dissociation. These findings contribute to the understanding of RNA-mediated intrinsic transcription termination.
Article
Chemistry, Analytical
Shuai Wang, Liyan Zhang, Ailing Kan, Xiaowen Xu, Nan Zhang, Wei Jiang
Summary: In this study, a MnO2 nanosheet-mediated target-binding-induced fluorescence resonance energy transfer (FRET) strategy was developed for detection and imaging of multiplexed miRNAs in living cells. The strategy successfully enabled simultaneous imaging of miRNA-373 and miRNA-96 in MDA-MB-231 and L02 cells, revealing higher expression levels of target miRNAs in MDA-MB-231 cells compared to L02 cells. This approach provides an alternative method for simultaneous accurate detection and imaging of multiplexed miRNAs with potential biomedical applications.
Article
Plant Sciences
Bao-Qiang Zheng, Xiao-Qing Li, Yan Wang
Summary: Orchid flowers have a unique structure with three sepals and three petals, and the lip is formed by one of the petals. The emission of floral scent in orchids is specific and spatially complex. This study investigated the molecular and biochemical mechanisms behind the differing scent emissions from different parts of orchid flowers, using the Cattleya hybrid KOVA as a model. The findings provide insights into the differences in scents between different flower parts and offer information for breeding orchid cultivars with special floral scents.
Review
Pathology
Yijuan Xing, Xiaolei Liang, Xiao Lv, Yuemei Cheng, Junhong Du, Chang Liu, Yongxiu Yang
Summary: Ovarian cancer is a highly aggressive tumor in women with poor prognosis and high mortality, while circular RNAs have shown potential as biomarkers in cancer research. The expression profiles of circRNAs in OC tissues suggest their involvement in various biological processes.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Review
Pathology
Yijuan Xing, Xiaolei Liang, Xiao Lv, Yuemei Cheng, Junhong Du, Chang Liu, Yongxiu Yang
Summary: This article summarizes the expression profiles of circRNAs in ovarian cancer tissues and discusses their regulatory role in multiple biological processes. It is found that circRNAs play a crucial role in the regulation of cell proliferation, apoptosis, migration, invasion, and other processes, and can serve as potential biomarkers for cancer.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Multidisciplinary Sciences
Man Pan, Qingyun Zheng, Tian Wang, Lujun Liang, Junxiong Mao, Chong Zuo, Ruichao Ding, Huasong Ai, Yuan Xie, Dong Si, Yuanyuan Yu, Lei Liu, Minglei Zhao
Summary: This study reveals the mechanism of the N-degron pathway mediated by Ubr1, including key structural elements involved in the initiation and elongation steps of ubiquitination.
Article
Biochemistry & Molecular Biology
Ines Simeone, Carmela Rubolino, Teresa Maria Rosaria Noviello, Diego Farinello, Luigi Cerulo, Matteo Jacopo Marzi, Francesco Nicassio
Summary: TDMDfinder is a computational pipeline that identifies TDMD interactions in the Human and Mouse transcriptomes. The study found that TDMD is widespread, with potentially every miRNA controlled by endogenous targets. Experimental validation and computational analysis suggested TDMD's involvement in human cancer and highlighted it as a potential oncogenic mechanism.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Eleonora Sarantelli, Apostolis Mourkakis, Lefteris C. Zacharia, Andreas Stylianou, Vasiliki Gkretsi
Summary: As metastasis is a major cause of cancer-related deaths, understanding the cellular and molecular events involved in cancer cell migration and invasion is crucial for developing novel anti-metastatic therapies. Fascin-1, an actin-bundling protein, plays a fundamental role in cell migration processes. It is significantly elevated in most cancers and its high expression is associated with aggressive disease and poor prognosis. Recent studies show that Fascin-1 is critically involved in metastasis and suggest it as a promising target for anti-metastatic treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Byungil Kim, Sarah Arcos, Katherine Rothamel, Jeffrey Jian, Kristie L. Rose, W. Hayes McDonald, Yuqi Bian, Seth Reasoner, Nicholas J. Barrows, Shelton Bradrick, Mariano A. Garcia-Blanco, Manuel Ascano
Article
Multidisciplinary Sciences
Caroline Wiser, Byungil Kim, Jessica Vincent, Manuel Ascano
SCIENTIFIC REPORTS
(2020)
Article
Biotechnology & Applied Microbiology
Min Guo, Yue Li, Yijun Su, Talley Lambert, Damian Dalle Nogare, Mark W. Moyle, Leighton H. Duncan, Richard Ikegami, Anthony Santella, Ivan Rey-Suarez, Daniel Green, Anastasia Beiriger, Jiji Chen, Harshad Vishwasrao, Sundar Ganesan, Victoria Prince, Jennifer C. Waters, Christina M. Annunziata, Markus Hafner, William A. Mohler, Ajay B. Chitnis, Arpita Upadhyaya, Ted B. Usdin, Zhirong Bao, Daniel Colon-Ramos, Patrick La Riviere, Huafeng Liu, Yicong Wu, Hari Shroff
NATURE BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Amir K. Foroushani, Bryan Chim, Madeline Wong, Andre Rastegar, Patrick T. Smith, Saifeng Wang, Kent Barbian, Craig Martens, Markus Hafner, Stefan A. Muljo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Rebecca S. Brown, Dimitrios G. Anastasakis, Markus Hafner, Margaret Kielian
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Byungil Kim, Sarah Arcos, Katherine Rothamel, Manuel Ascano
Summary: The VIR-CLASP method uses 4SU labeling and protein crosslinking to identify primary viral RNA-host protein interactions. It allows for the investigation of a wide range of RNA viruses and provides a strategy for revealing host protein and viral RNA interactions.
Article
Biochemistry & Molecular Biology
Dimitrios G. Anastasakis, Alexis Jacob, Parthena Konstantinidou, Kazuyuki Meguro, Duncan Claypool, Pavol Cekan, Astrid D. Haase, Markus Hafner
Summary: CLIP methods, particularly PAR-CLIP, allow for the interrogation of direct protein-RNA interactions and gene regulatory networks. This technique utilizes photoreactive nucleosides to crosslink interacting molecules, offering a high sensitivity and specificity in pinpointing RNA binding sites.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Yutaka Enomoto, Peng Li, Lisa M. Jenkins, Dimitrios Anastasakis, Gaelyn C. Lyons, Markus Hafner, Warren J. Leonard
Summary: NK-EVs derived from IL-15 + IL-21 stimulated NK-92 cells show enhanced cytotoxic capacity against tumor cells, with CD226 playing a key role. However, enrichment of cytolytic granules granzyme B and granzyme H is not the key factor contributing to the enhanced cytotoxic activity.
CANCER GENE THERAPY
(2022)
Article
Cell Biology
Mark Sauer, Nina Was, Thomas Ziegenhals, Xiantao Wang, Markus Hafner, Matthias Becker, Utz Fischer
Summary: The miR-26 family acts as a trigger for a self-amplifying system required for neural differentiation by directly targeting Rest, inducing the expression of neuronal genes, and halting neurogenesis at the neural progenitor level. This identification sheds light on the molecular events triggered by miR-26 in regulating neurogenesis.
JOURNAL OF CELL SCIENCE
(2021)
Review
Virology
Samantha Lisy, Katherine Rothamel, Manuel Ascano
Summary: RBPs, as intracellular host factors that interact with RNA virus genomes, have a profound impact on infection outcomes. Recent discoveries from new methodologies have led to a reevaluation of RBPs and post-transcriptional gene regulation, highlighting how RBPs can impact the fates of cellular and viral RNA in conflicting ways. Noncanonical RBPs, initially characterized through interactions with viral RNA, may have roles beyond viral pathogenesis, challenging the discrimination between cellular and viral RNA for exerting either pro- or antiviral effects.
Article
Immunology
Kyle M. Garland, Jonah C. Rosch, Carcia S. Carson, Lihong Wang-Bishop, Ann Hanna, Sema Sevimli, Casey Van Kaer, Justin M. Balko, Manuel Ascano, John T. Wilson
Summary: Nucleic acids mislocalized within cells can trigger immune responses, and NanoISD has been developed to overcome delivery barriers of ISD and promote antitumor immunity by activating cGAS.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Dan Cheng, Kevin Semmens, Elizabeth McManus, Qingrong Chen, Daoud Meerzaman, Xiantao Wang, Markus Hafner, Brian A. Lewis, Hidehisa Takahashi, Ballachanda N. Devaiah, Anne Gegonne, Dinah S. Singer
Summary: TAF7, a component of TFIID, is identified as a previously unknown RNA chaperone that contributes to the regulation of protein synthesis by binding a broad spectrum of target RNA species and delivering them to cytoplasmic polysomes. The export of TAF7-bound RNAs to the cytoplasm is dependent on a TAF7 nuclear export signal and an exportin 1-dependent pathway. Disruption of either TAF7's RNA binding or its nuclear export leads to retention of target messenger RNAs in the nucleus and reduced protein levels of TAF7-target RNAs.
Article
Biochemistry & Molecular Biology
Yingxiao Chen, Yanping Li, Roselyn S. Dai, Jonathan C. Savage, Ujwal Shinde, John Klimek, Larry L. David, Emma A. Young, Markus Hafner, Rosalie C. Sears, Xiao-Xin Sun, Mu-Shui Dai
Summary: The RNA exosome is regulated by the nucleolar ubiquitin-specific protease USP36 through direct interaction with the exonuclease EXOSC10 in the nucleolus. USP36 promotes the SUMOylation of EXOSC10 at lysine (K) 583, which is critical for the function of the RNA exosome in ribosome biogenesis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Katherine Rothamel, Sarah Arcos, Byungil Kim, Clara Reasoner, Samantha Lisy, Neelanjan Mukherjee, Manuel Ascano
Summary: Research has shown that ELAVL1 transitions its binding sites upon cell immune stimulation and mediates RNA stability of genes regulating pathogen sensing and cytokine production pathways.
Article
Multidisciplinary Sciences
Markus Hafner, Maria Katsantoni, Tino Koester, James Marks, Joyita Mukherjee, Dorothee Staiger, Jernej Ule, Mihaela Zavolan
Summary: This article discusses the process of RNA assembly into RNP complexes and introduces the techniques for identifying the binding sites of RNA-binding proteins through CLIP and other methods. It also covers the challenges of computational CLIP data analysis, handling background sources, and identifying binding regions, as well as the prospect of integrating different methods to gain a comprehensive view.
NATURE REVIEWS METHODS PRIMERS
(2021)
