Article
Biochemistry & Molecular Biology
Margaret L. Rodgers, Brett O'Brien, Sarah A. Woodson
Summary: sRNPs play key roles in guiding the folding, modification, and splicing of nascent precursor RNAs during transcription. However, the rapid co-transcriptional folding of RNA can hinder the recognition and regulation of sRNP binding sites. In this study, the binding of Hfq•DsrA sRNPs to rpoS transcripts was examined using the single-molecule co-localization co-transcriptional assembly (smCoCoA) technique. It was found that Hfq•DsrA samples the mRNA before the transcription of the target site, preparing it for base pairing with DsrA. Furthermore, it was observed that Hfq•DsrA often binds to the mRNA close to RNA polymerase (RNAP) during the synthesis of the target site. This suggests that targeting transcripts near RNAP allows sRNPs to capture the site before the RNA folds, providing a kinetic advantage in recognition and regulation.
Article
Biology
Florian Turbant, Pengzhi Wu, Frank Wien, Veronique Arluison
Summary: This study focuses on the bacterial amyloid protein Hfq, revealing that its amyloid region significantly influences the annealing efficiency between small noncoding RNA and mRNA. The unexpected finding suggests a potential novel physiological role of amyloids, including those associated with neurodegenerative diseases.
Article
Cell Biology
Alisia Made, Alessia Bibi, Jose Manuel Garcia-Manteiga, Anna Sofia Tascini, Santiago Nicolas Piella, Roman Tikhomirov, Christine Voellenkle, Carlo Gaetano, Przemyslaw Leszek, Serenella Castelvecchio, Lorenzo Menicanti, Fabio Martelli, Simona Greco
Summary: This study aims to explore the role of noncoding RNAs in cardiovascular diseases. The research found that circular RNAs can interact with microRNAs, regulating the expression of cardiovascular disease-related signaling pathways. Specifically, the study found that circBPTF is upregulated under hypoxia conditions and can regulate the function of endothelial cells by targeting miRNA targets such as HDAC9 and LRRC17.
Article
Plant Sciences
Ning Li, Tongtong Liu, Feng Guo, Jinwen Yang, Yugang Shi, Shuguang Wang, Daizhen Sun
Summary: This study identified lncRNAs, miRNAs, and genes related to drought stress in wheat through whole-transcriptome sequencing and explored their regulatory modules. The results revealed the potential role of these regulatory modules in wheat drought tolerance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Fei Wang, Qianqian Wang, Baowei Liu, Lisheng Mei, Sisi Ma, Shujuan Wang, Ruoyu Wang, Yan Zhang, Chaoshi Niu, Zhiqi Xiong, Yong Zheng, Zhi Zhang, Juan Shi, Xiaoyuan Song
Summary: The highly expressed lncRNA Synage in the cerebellum regulates synaptic stability through multiple mechanisms, including serving as a sponge for microRNA miR-325-3p and as a scaffold for organizing protein complexes in synapses. Deletion of Synage leads to a spectrum of cerebellar abnormalities in mice, ultimately resulting in motor dysfunction in adults.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Cell Biology
Qian Zhang, Yun-Fei Yan, Qing Lv, You-Jie Li, Ran-Ran Wang, Guang-Bin Sun, Li Pan, Jin-Xia Hu, Ning Xie, Can Zhang, Bao-Cheng Tian, Fei Jiao, Sen Xu, Ping-Yu Wang, Shu-Yang Xie
Summary: miR-4293 plays an important role in lung carcinoma by upregulating WFDC21P expression through DCP2 regulation. The interaction between miR-4293 and WFDC21P in promoting lung carcinoma suggests potential therapeutic targets and diagnostic markers.
CELL DEATH & DISEASE
(2021)
Editorial Material
Oncology
Barbara Pardini, Mihnea P. Dragomir
Summary: The study by Zagorac et al. unveils a novel molecular mechanism in breast cancer involving SOX2, EZH2, and the long noncoding RNA SCIRT. Upregulation of SCIRT may lead to the dedifferentiation of TICs into a less tumorigenic phenotype and offer new therapeutic opportunities.
Article
Biochemistry & Molecular Biology
Shuwei Ren, Ning Zhang, Liping Shen, Yongyong Lu, Yixin Chang, Zhenni Lin, Ning Sun, Yuanmei Zhang, Jiheng Xu, Haishan Huang, Honglei Jin
Summary: The study found that the long noncoding RNA lnc00892 is significantly downregulated in bladder cancer tissues and its low expression is associated with poor prognosis. Lnc00892 was shown to inhibit migration, invasion, and metastasis of bladder cancer cells by reducing nucleolin gene transcription and inhibiting nucleolin-mediated stabilization of RhoA/RhoC mRNA. These findings suggest that lnc00892 may serve as a potential therapeutic target for invasive bladder cancer patients.
Article
Chemistry, Multidisciplinary
Runnan Zhang, Shiqun Shao, Ying Piao, Jiajia Xiang, Xuyong Wei, Zhen Zhang, Zhuxian Zhou, Jianbin Tang, Nasha Qiu, Xiao Xu, Yanpeng Liu, Youqing Shen
Summary: This study reports the development of new lipid nanoparticles with high delivery efficiency and improved storage stability through the rational design and combinatorial synthesis of esterase-triggered decationizable quaternium lipid-like molecules. The optimized nanoparticles enable efficient mRNA transfection and selective induction of antigen-specific immune responses in the spleen.
ADVANCED MATERIALS
(2023)
Article
Genetics & Heredity
Bing Wang, Jun Wu, Qilin Huang, Xiaohui Yuan, Yi Yang, Wen Jiang, Yi Wen, Lijun Tang, Hongyu Sun
Summary: The study revealed that both lncRNAs and circRNAs play crucial roles in the pathogenesis of SAP, providing new insights for further exploration of the disease mechanism and target discovery in SAP.
FRONTIERS IN GENETICS
(2021)
Article
Immunology
Xiuhong Sun, Yishan Liu, Xinyu Gao, Mengxuan Du, Mengge Gao, Xingming Zhong, Xiangcai Wei
Summary: This study revealed aberrant expression profiles of mRNAs and lncRNAs in the peripheral blood of PCOS patients, with lncRNA-mRNA pairs in chemokine signaling pathway potentially playing a role in the genetic mechanism of PCOS.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Daria Konina, Peter Sparber, Iuliia Viakhireva, Alexandra Filatova, Mikhail Skoblov
Summary: In this study, the widely expressed lncRNA LINC00493 was investigated for its structural characteristics, cellular localization, and impact on cell physiology. The results showed that LINC00493 has a cell-type-specific influence on cell viability and that its sORF translated into small protein SMIM26 affects cell viability in an opposite manner.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Mathematical & Computational Biology
Xudan Ma, Qijun Zhang, Haihong Zhu, Kefeng Huang, Weina Pang, Qin Zhang
Summary: The study established an HF-related ceRNA network based on lncRNA, miRNA, and mRNA, revealing the importance of certain lncRNA as hub nodes. Five subnetworks were formed around miR-17-5p, miR-20b-5p, miR107, miR-125a-5p, and miR-140-5p, with enrichment in cell cycle pathways observed in the ceRNA network. The research sheds new light on the essential functions of the ceRNA network in HF development and suggests potential diagnostic and therapeutic applications of hub nodes.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Jian-Rong Li, Mabel Tang, Yafang Li, Christopher Amos, Chao Cheng
Summary: In this study, a computational framework was proposed to infer mRNA stability of genes using RNA-seq data and identify stQTLs. The results revealed that stQTLs were enriched in the CDS and 3'UTR regions, while eQTLs were enriched in multiple regions. Additionally, stQTLs were more likely to overlap with RNA binding protein and microRNA binding sites. This study demonstrates that simultaneous identification of stQTLs and eQTLs provides more mechanistic insight into the association between genetic variants and gene expression levels.
Article
Biochemical Research Methods
Chen Shen, Huiyu Li, Miao Li, Yu Niu, Jing Liu, Li Zhu, Hongsheng Gui, Wei Han, Huiying Wang, Wenpei Zhang, Xiaochen Wang, Xiao Luo, Yu Sun, Jiangwei Yan, Fanglin Guan
Summary: The lack of a reliable and easy-to-operate screening pipeline for disease-related noncoding RNA regulatory axis is a problem that needs urgent solution. In this study, we designed a hybrid pipeline called DLRAPom, which combines conventional bioinformatics analysis, experimental validation, and a novel machine learning model to identify risk biomarkers and disease-related noncoding RNA regulatory axes. Using the pipeline, we predicted several risk protein-coding biomarkers and regulatory axes related to gestational diabetes mellitus (GDM). Overall, DLRAPom is a flexible pipeline that can contribute to molecular pathogenesis research and provide potential candidates for functional research on disease pathogenesis.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Helga U. van der Heul, Bohdan L. Bilyk, Kenneth J. McDowall, Ryan F. Seipke, Gilles P. van Wezel
NATURAL PRODUCT REPORTS
(2018)
Article
Biotechnology & Applied Microbiology
Ander Hernandez Plagaro, Peter B. Pearman, Vladimir R. Kaberdin
Article
Multidisciplinary Sciences
Itxaso Montanchez, Elixabet Ogayar, Ander Hernandez Plagaro, Anna Esteve-Codina, Jessica Gomez-Garrido, Maite Orruno, Ines Arana, Vladimir R. Kaberdin
SCIENTIFIC REPORTS
(2019)
Article
Public, Environmental & Occupational Health
Z. Bravo, M. Orruno, T. Navascues, E. Ogayar, J. Ramos-Vivas, V. R. Kaberdin, I Arana
JOURNAL OF HOSPITAL INFECTION
(2019)
Article
Ecology
Maite Orruno, Claudia Parada, Elixabet Ogayar, Vladimir R. Kaberdin, Ines Arana
AQUATIC MICROBIAL ECOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Anna Chao Kaberdina, Olatz Ruiz-Larrabeiti, Sue Lin-Chao, Vladimir R. Kaberdin
MOLECULAR GENETICS AND GENOMICS
(2019)
Correction
Biochemistry & Molecular Biology
Anna Chao Kaberdina, Olatz Ruiz-Larrabeiti, Sue Lin-Chao, Vladimir R. Kaberdin
MOLECULAR GENETICS AND GENOMICS
(2019)
Article
Environmental Sciences
Itxaso Montanchez, Vladimir R. Kaberdin
MARINE ENVIRONMENTAL RESEARCH
(2020)
Article
Microbiology
Maite Orruno, Claudia Parada, Vladimir R. Kaberdin, Ines Arana
Summary: The study revealed that exposure to visible light reduces the culturability of Vibrio harveyi, likely leading to entry into the Viable but Non Culturable state (VBNC), while populations kept in darkness remained culturable for at least 21 days. Despite differences, both starved cell populations showed morphological changes by reducing their size. Furthermore, proteomic analysis indicated changes in cell envelope composition that may account for the different adaptation patterns observed in the absence and presence of visible light.
Article
Environmental Sciences
Elixabet Ogayar, Irene Larranaga, Ana Lomba, Vladimir R. Kaberdin, Ines Arana, Maite Orruno
Summary: Vibrio is a widely distributed bacterial genus, with climate change potentially increasing the incidence of Vibrio-associated diseases worldwide. Conventional culture-based methods may underestimate cell numbers, while using CARD-FISH can overcome this issue and improve the detection sensitivity and selectivity of marine vibrios.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Gunn-Guang Liou, Anna Chao Kaberdina, Wei-Syuan Wang, Vladimir R. Kaberdin, Sue Lin-Chao
Summary: By analyzing the physiology and gene expression of E. coli in low-oxygen environments, we identified genes involved in acid-stress adaptation, cell adhesion/biofilm formation, electron transport, oligopeptide transport, and anaerobic respiration/fermentation that are upregulated under microaerobic conditions. In contrast, genes involved in iron transport, aerobic respiration, and de novo nucleotide synthesis were downregulated. We also discovered and discussed the regulatory functions of differentially expressed noncoding small RNAs during microaerobic growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Daniel Fernandez-Remacha, Candela Gonzalez-Riancho, Miranda Lastra Osua, Aranzazu Gonzalez Arce, Itxaso Montanchez, Juan Maria Garcia-Lobo, Roger Estrada-Tejedor, Vladimir R. Kaberdin
Summary: Researchers isolated fungal strains producing laccases from a cave in northern Spain, identifying them as Gliomastix murorum and Conidiobolus thromboides. Further analysis showed that the laccases secreted by these fungi could degrade various industrial dyes. The study suggests promising applications of these enzymes in biotechnology.
Article
Biochemistry & Molecular Biology
Justin E. Clarke, Kiran Sabharwal, Louise Kime, Kenneth J. McDowall
Summary: RNase E is an endoribonuclease that plays a crucial role in the maturation of RNA involved in translation and mRNA degradation. It binds to structured RNA elements, activating catalysis and facilitating tRNA processing and potential mRNA degradation. The recognition of structured elements is mediated by a newly discovered groove, essential for E. coli cell viability and distinct from the RNase G family.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Asier Ramos-Pardo, Rocio Castro-Alvarez, Guillermo Quindos, Elena Eraso, Elena Sevillano, Vladimir R. Kaberdin
Summary: This study aimed to investigate the impact of external pH, substrate nature, and strain origin on the production of protease, lipase, and hemolysin in Candida albicans. The pH value had a significant effect on the detection of protease and lipase, while the activity of hemolysin was not affected by pH. Additionally, the anatomical origin of the isolates was found to be associated with the detected activities.
Article
Microbiology
Oleg N. Murashko, Kun-Hai Yeh, Chen-Hsin Albert Yu, Vladimir R. Kaberdin, Sue Lin-Chao
Summary: This study demonstrates that fluoride can impact gene expression posttranscriptionally by slowing down RNA degradation, thereby enhancing RNA stability and steady-state mRNA levels in E. coli.
MICROBIOLOGY SPECTRUM
(2023)