Article
Biochemistry & Molecular Biology
Pauline Francois, Hugo Arbes, Stephane Demais, Agnes Baudin-Baillieu, Olivier Namy
Summary: Ribosome profiling, a powerful tool for studying translation regulation, suffers from a lack of standardization in the bioinformatics part, hindering result reproducibility. A unique tool has been proposed to standardize the general steps of RiboSeq analysis, aiming to unify bioinformatics pipelines for translation research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Jia-Xin Chen, Shu He, Yan-Jun Wang, Xiong-Kang Gan, Ya-Qing Zhou, Lei Hua, Can Hou, Sheng Zhang, Han-Xiao Zhou, En-Zhi Jia
Summary: This study aimed to investigate mRNA expression profiling in CAD patients and identified BTRC and UBE2D2 genes as potential diagnostic biomarkers with significant diagnostic values. The study highlights the potential of these genes as novel diagnostic biomarkers and therapeutic targets for CAD.
Review
Endocrinology & Metabolism
Chao Jiang, Zhe Chen, Xiaohui Wang, Yongyuan Zhang, Xinyu Guo, Zhengwei Xu, Hao Yang, Dingjun Hao
Summary: Low back pain is a common musculoskeletal symptom that severely affects quality of life. Intervertebral disc degeneration is considered a major cause, and non-coding RNAs play crucial roles in its development. Their potential as therapeutic targets for IDD remain to be explored.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Review
Gastroenterology & Hepatology
Jia-Li Shao, Li-Juan Wang, Ji Xiao, Jin-Feng Yang
Summary: Hepatic ischemia-reperfusion injury (HIRI) is a major complication of liver surgery and transplantation, with significant impact on postoperative outcomes. The underlying mechanisms involve oxidative stress, inflammatory responses, immunoreactions, and cell death. Non-coding RNAs (ncRNAs) have emerged as important players in HIRI, with differential expression and involvement in pathological processes. Some ncRNAs have been identified as biomarkers for early diagnosis and assessment of liver damage severity, as well as potential therapeutic targets for attenuating HIRI. However, further studies are needed to fully understand the therapeutic potential and feasibility of clinical application.
WORLD JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Multidisciplinary Sciences
Karim Rahimi, Morten T. Veno, Daniel M. Dupont, Jorgen Kjems
Summary: Circular RNAs, a class of covalently joined non-coding RNAs, play functional roles in cellular processes and exhibit overlap with exons in linear mRNAs. Long-read sequencing techniques have been used to characterize circRNAs, revealing a large number of splicing events and proposing altered exon usage as a resistance mechanism to nonsense-mediated decay. The development of targeted long-read sequencing methods offers a comprehensive approach to understanding the structure and function of circRNAs.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Alla D. Fedorova, Jack A. S. Tierney, Audrey M. Michel, Pavel V. Baranov
Summary: Ribo-Seq is a technology that captures the locations of ribosomes in the entire transcriptome, providing insights into gene expression and discovering novel translated regions. RiboGalaxy is a Galaxy-based platform for processing Ribo-Seq data, with links to Riboseq.Org resources and other tools to improve data analysis interoperability.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Chiara Siracusa, Jolanda Sabatino, Isabella Leo, Ceren Eyileten, Marek Postula, Salvatore De Rosa
Summary: Lack of timely intervention strategies for acute ischemic stroke due to limited understanding of underlying mechanisms. Circular RNAs involved in pathophysiological processes of ischemic stroke, providing potential therapeutic targets and clinical biomarkers.
Article
Pharmacology & Pharmacy
Shasha Zhang, Fangyi Long, Hong Lin, Xi Wang, Gang Jiang, Ting Wang
Summary: Circular RNAs (circRNAs) play a crucial role in chronic diseases, and phytochemicals regulate their expression and biological functions, impacting cell processes by acting as miRNA sponges and affecting miRNA-mediated regulation of target genes.
PHARMACOLOGICAL RESEARCH
(2021)
Review
Medicine, General & Internal
Yachen Shi, Qingyun Wang, Ruize Song, Yan Kong, Zhijun Zhang
Summary: Non-coding RNAs, such as microRNAs, circular RNAs, and long non-coding RNAs, play important roles in regulating normal biological processes and may be implicated in the pathogenesis of human diseases like depression. Clinical studies have shown that abnormal expression of ncRNAs in depressed patients compared to healthy individuals, with potential for ncRNAs to serve as biomarkers for diagnosis and treatment. Despite uncertainties regarding their precise roles, ncRNAs demonstrate promising clinical value in the management of depression.
Article
Biochemistry & Molecular Biology
Jing Liu, Liling Niu, Jiaru Hao, Yuan Yao, Meinan Yan, Hui Li
Summary: Circular RNA (circRNA) is a unique RNA molecule with a closed loop structure. In gastric cancer patients, circIPO7 is downregulated and its overexpression inhibits cancer cell proliferation by blocking the interaction between caprin-1 and G3BP1, leading to the translational inhibition of EGFR and mTOR through the PI3K/AKT/mTOR pathway.
Review
Oncology
Yueyue Wang, Qian Liu, Fengchao Wang
Summary: Chemoresistance is a common issue in various types of tumors, leading to cancer relapse. Non-coding RNAs, especially those carried by exosomes, play crucial roles in mediating chemoresistance and cell-to-cell communication in cancer.
Article
Biochemistry & Molecular Biology
Stefan Oberlin, Rajendran Rajeswaran, Marieke Trasser, Veronica Barragan-Borrero, Michael A. Schon, Alexandra Plotnikova, Lukas Loncsek, Michael D. Nodine, Arturo Mari-Ordonez, Olivier Voinnet
Summary: The co-evolution between hosts' and parasites' genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, the translation of short subgenomic mRNA (shGAG) during ribosomal stalling triggers a translation-dependent silencing (TdS) response that serves as a primary defense against de novo invasions.
Review
Biochemistry & Molecular Biology
Sonia Chothani, Lena Ho, Sebastian Schafer, Owen Rackham
Summary: Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Ribo-seq overcomes limitations of traditional methods and provides more comprehensive information. However, challenges such as data quality, depth, and sparseness need to be addressed for establishing a canonical catalogue of translated smORFs.
Review
Oncology
Tingsong Chen
Summary: Hepatocellular carcinoma is the second leading cause of cancer-related deaths worldwide. Traditional diagnostic methods have low sensitivity and the disease is often diagnosed at a late stage. Non-coding RNAs provide new insights for early diagnosis.
JOURNAL OF HEPATOCELLULAR CARCINOMA
(2022)
Article
Biotechnology & Applied Microbiology
Xiaoyu Yang, Bo Song, Jie Cui, Lina Wang, Shuoshuo Wang, Linlin Luo, Lei Gao, Beixin Mo, Yu Yu, Lin Liu
Summary: This study reveals that translational reprogramming plays an important role in rice's response to salt stress, with the salt-tolerant cultivar SR86 adopting a more flexible translational adaptive strategy compared to the salt-sensitive cultivar NB. The differences in translational dynamics under salt stress between NB and SR86 may be due to their varying levels of ribosome stalling.
Article
Genetics & Heredity
Hua Rao, Xiao-Juan Wang, Jian-Xiang Ma, Qi-En Li, Guang-Lin Li, Jia-Bin Zou
MITOCHONDRIAL DNA PART B-RESOURCES
(2018)
Article
Biochemistry & Molecular Biology
Minta Chaiprasongsuk, Chi Zhang, Ping Qian, Xinlu Chen, Guanglin Li, Robert N. Trigiano, Hong Guo, Feng Chen
Article
Biochemistry & Molecular Biology
Lulu Xu, Zhiqiang Hao, Jinyan Lin, Qiong Zhao, Baojun Zhang, Guanglin Li, Jianping He, Jingang Li
MOLECULAR BIOLOGY REPORTS
(2019)
Article
Plant Sciences
Hao Chen, Tobias G. Koellner, Guanglin Li, Guo Wei, Xinlu Chen, Dali Zeng, Qian Qian, Feng Chen
Article
Biochemistry & Molecular Biology
Jingjing Zhang, Ruiqi Liu, Yanfeng Zhu, Jiaxin Gong, Shuwei Yin, Peisen Sun, Hao Feng, Qi Wang, Shuaijing Zhao, Zhongyuan Wang, Guanglin Li
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Ziyad Tariq Muhseen, Guanglin Li
Article
Genetics & Heredity
Peisen Sun, Haoming Wang, Guanglin Li
FRONTIERS IN GENETICS
(2020)
Article
Chemistry, Physical
Ziyad Tariq Muhseen, Alaa R. Hameed, Halah M. H. Al-Hasani, Muhammad Tahir ul Qamar, Guanglin Li
JOURNAL OF MOLECULAR LIQUIDS
(2020)
Article
Biochemistry & Molecular Biology
Ziyad Tariq Muhseen, Alaa R. Hameed, Halah M. H. Al-Hasani, Sajjad Ahmad, Guanglin Li
Summary: The study identified natural compounds like glycyrrhizin as potential therapeutic options against SARS-CoV-2, demonstrating stable binding and strong affinity within the virus enzymes through docking experiments and molecular dynamics simulations.
Article
Environmental Sciences
Ziyad Tariq Muhseen, Mustafa Hussein Ali, Nawar Rushdi Jaber, Dheyaa Shakir Mashrea, Ali Mamoon Alfalki, Guanglin Li
Summary: The OGG1 enzyme plays a crucial role in inflammation, anti-cancer and neurodegenerative diseases. Through screening drug libraries, two potential anti-cancer compounds were found to stably bind to the active pocket of OGG1 with higher affinity compared to the control. The binding affinity and molecular dynamics simulations of the compounds were validated, supporting their candidacy for anti-cancer activities.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Biochemistry & Molecular Biology
K. Zhou, Q. -X. Cao, C. -M. Jin, Y. -Y. Niu, G. -L. Li, J. -J. Zhang