Article
Plant Sciences
Yangang Lan, Kaimei Zhang, Ting He, Hao Wang, Chengzhi Jiang, Hanwei Yan, Yan Xiang
Summary: This study conducted a comprehensive analysis and functional research of SRs in poplar and other dicots, revealing the important role of a key gene PtSC27 in salt stress response. Overexpression of PtSC27 enhanced plant tolerance to salt stress by regulating enzyme activities and gene expression. These findings provide a foundation for understanding the structure and function of SRs and offer important gene resources for genetic engineering breeding.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Agriculture, Multidisciplinary
Xiao-wen Ma, Qiu-xiang Ma, Mu-qing Ma, Yan-hang Chen, Jin-bao Gu, Yang Li, Qing Hu, Qing-wen Luo, Ming-fu Wen, Peng Zhang, Cong Li, Zhen-yu Wang
Summary: Soil salinity affects the alternative splicing of serine/arginine-rich (SR) genes and isoforms, which regulates plant adaptation to stress. In this study, we analyzed 37 genes of the RS subfamily from 11 plant species and found that RS subfamily genes play important functional roles in response to abiotic stresses. Overexpression of MeRS40 enhanced salt tolerance in Arabidopsis by maintaining ROS homeostasis and up-regulating salt-responsive genes, while in cassava, overexpression of MeRS40 reduced salt tolerance due to negative autoregulation. The MeRS40 protein interacted with MeU1-70Ks, suggesting its involvement in post-transcriptional regulation.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Pharmacology & Pharmacy
Dan Hua, Qian Zhao, Yang Yu, Huan Yu, Lin Yu, Xuexia Zhou, Qian Wang, Cuiyun Sun, Cuijuan Shi, Wenjun Luo, Zhendong Jiang, Weiting Wang, Lingli Wang, Dongli Zhang, Shengan Tang, Shizhu Yu
Summary: Eucalyptal A is identified as an important lead compound with anti-glioblastoma activity, inhibiting cell proliferation and invasiveness to prolong overall survival time, and exerting anti-tumor effects through modulation of relevant pathways.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Oncology
Jingsheng Yuan, Zijian Liu, Zhenru Wu, Jiayin Yang, Tao Lv
Summary: This study comprehensively evaluated the expression and prognostic significance of SRSF family genes in hepatocellular carcinoma (HCC). By establishing an SRSF score, the researchers found that this score was associated with the prognosis and drug sensitivity of HCC. Furthermore, they identified an important gene, SRSF11, whose silencing inhibited cell proliferation and enhanced drug sensitivity in HCC.
Review
Plant Sciences
Zi-Chang Jia, Debatosh Das, Youjun Zhang, Alisdair R. Fernie, Ying-Gao Liu, Moxian Chen, Jianhua Zhang
Summary: Serine/arginine-rich (SR) proteins participate in RNA processing and maintain plant growth and stress responses through interactions with precursor mRNAs or other splicing factors. SR proteins are crucial for alternative splicing and play essential roles in the composition and alternative splicing of precursor mRNAs. However, their evolutionary trajectory, molecular function, and regulatory network in plants are still largely unknown compared to their animal counterparts. This article reviews the current understanding of the SR protein family in eukaryotes and proposes potential key research priorities for future functional studies.
Article
Plant Sciences
Steven Fanara, Marie Schloesser, Marc Hanikenne, Patrick Motte
Summary: The mutant sr45-1 in Arabidopsis exhibits a phenotype of constitutive iron deficiency, characterized by iron accumulation in root tissues and iron starvation in aerial parts. RNA-Sequencing reveals severe perturbations in metal homeostasis, phenylpropanoid pathway, oxidative stress responses, and reproductive development. Some developmental abnormalities of sr45-1 can be complemented by exogenous iron supply.
Article
Plant Sciences
Shanlan Chen, Yujian Mo, Yingjie Zhang, Hongbao Zhu, Yu Ling
Summary: SR proteins from sweet potato have similar functional domains and gene structures as those from Arabidopsis and rice. However, their expression patterns and alternative splicing regulations have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes.
Review
Biochemistry & Molecular Biology
Kai Zheng, Zhe Ren, Yifei Wang
Summary: Accumulating evidence has confirmed the interaction between viral infection and host alternative splicing. Serine-arginine (SR) proteins and serine-arginine protein kinases (SRPKs) play critical roles in spliceosome maturation, alternative splicing, and RNA metabolism. Viral proteins, as well as other cytoplasmic proteins, have been identified as substrates of SRPKs, highlighting the importance of SRPKs in virus-host interactions. This review discusses the regulation and biological function of SRPKs, their involvement in viral infection processes, the structure-function relationships of SRPK inhibitors, and the potential of targeting viral proteins and cellular substrates of SRPKs for antiviral therapy.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Chaowei Wen, Zhujun Tian, Lan Li, Tongke Chen, Huajian Chen, Jichen Dai, Zhenzhen Liang, Shumei Ma, Xiaodong Liu
Summary: This study reveals the competitive antagonistic interaction of SRSF3 and HNRNPH1 in regulating the alternative splicing of PRMT5 induced by ionizing radiation (IR). Downregulation of SRSF3 leads to an increased level of PRMT5-ISO5, which enhances cancer cell radiosensitivity. In vivo experiments confirm that IR induces increased levels of PRMT5-ISO5, which in turn enhances tumor killing and regression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Zhongliang Xu, Ning Zhang, Haiquan Fu, Fuyou Wang, Mingfu Wen, Hailong Chang, Jiantao Wu, Walid Badawy Abdelaala, Qingwen Luo, Yang Li, Cong Li, Qinnan Wang, Zhen-Yu Wang
Summary: This study identified stress-related genes and differentially alternative splicing (DAS) events in date palm under salt stress conditions. The salt overly sensitive (SOS) pathway genes were found to be involved in the regulation of salt response in date palm. The spliceosome pathway was enriched in the upregulated category, suggesting its potential role in salt stress response. The study highlights the pivotal role of alternative splicing (AS) in regulating salt stress and provides novel insights for enhancing salt resistance in date palm.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Qiuxia Yan, Peng Zeng, Xiuqin Zhou, Xiaoying Zhao, Runqiang Chen, Jing Qiao, Ling Feng, Zhenjie Zhu, Guozhi Zhang, Cairong Chen
Summary: The study revealed that RBMX is significantly downregulated in bladder cancer tissues and inhibits tumorigenicity and progression through interfering with PKM alternative splicing. This suggests RBMX may serve as a novel prognostic biomarker for clinical intervention in bladder cancer.
Article
Biochemistry & Molecular Biology
Xijuan Zhao, Lingling Tan, Shuo Wang, Yirong Shen, Liangyu Guo, Xiaoxue Ye, Shenkui Liu, Ying Feng, Wenwu Wu
Summary: This study identified 24 PtSR genes in Popolus trichocarpa, showing their constitutive expression in roots, stems, and leaves, and their response to various stresses. PtSCL30 may act as a negative regulator under cold and salt stress in woody plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Microbiology
Florentin Pastor, Lulzim Shkreta, Benoit Chabot, David Durantel, Anna Salvetti
Summary: Protein phosphorylation is crucial in regulating protein half-life, intracellular distribution, and activity, with CMGC kinases playing a key role in gene expression through splicing control. These kinases, belonging to different families, also influence viral replication, indicating potential translational opportunities.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Allison R. Wagner, Chi G. Weindel, Kelsi O. West, Haley M. Scott, Robert O. Watson, Kristin L. Patrick, Kristen W. Lynch
Summary: This study reveals the role of SRSF6 in regulating mitochondrial homeostasis and the macrophage's response to pathogens through alternative splicing of BAX.
Article
Genetics & Heredity
Urmo Vosa, Annique Claringbould, Harm-Jan Westra, Marc Jan Bonder, Patrick Deelen, Biao Zeng, Holger Kirsten, Ashis Saha, Roman Kreuzhuber, Seyhan Yazar, Harm Brugge, Roy Oelen, Dylan H. de Vries, Monique G. P. van der Wijst, Silva Kasela, Natalia Pervjakova, Isabel Alves, Marie-Julie Fave, Mawusse Agbessi, Mark W. Christiansen, Rick Jansen, Ilkka Seppala, Lin Tong, Alexander Teumer, Katharina Schramm, Gibran Hemani, Joost Verlouw, Hanieh Yaghootkar, Reyhan Sonmez Flitman, Andrew Brown, Viktorija Kukushkina, Anette Kalnapenkis, Sina Rueger, Eleonora Porcu, Jaanika Kronberg, Johannes Kettunen, Bernett Lee, Futao Zhang, Ting Qi, Jose Alquicira Hernandez, Wibowo Arindrarto, Frank Beutner, Julia Dmitrieva, Mahmoud Elansary, Benjamin P. Fairfax, Michel Georges, Bastiaan T. Heijmans, Alex W. Hewitt, Mika Kahonen, Yungil Kim, Julian C. Knight, Peter Kovacs, Knut Krohn, Shuang Li, Markus Loeffler, Urko M. Marigorta, Hailang Mei, Yukihide Momozawa, Martina Mueller-Nurasyid, Matthias Nauck, Michel G. Nivard, Brenda W. J. H. Penninx, Jonathan K. Pritchard, Olli T. Raitakari, Olaf Rotzschke, Eline P. Slagboom, Coen D. A. Stehouwer, Michael Stumvoll, Patrick Sullivan, Peter A. C. 't Hoen, Joachim Thiery, Anke Tonjes, Jenny van Dongen, Maarten van Iterson, Jan H. Veldink, Uwe Voelker, Robert Warmerdam, Cisca Wijmenga, Morris Swertz, Anand Andiappan, Grant W. Montgomery, Samuli Ripatti, Markus Perola, Zoltan Kutalik, Emmanouil Dermitzakis, Sven Bergmann, Timothy Frayling, Joyce van Meurs, Holger Prokisch, Habibul Ahsan, Brandon L. Pierce, Terho Lehtimaki, Dorret Boomsma, Bruce M. Psaty, Sina A. Gharib, Philip Awadalla, Lili Milani, Willem H. Ouwehand, Kate Downes, Oliver Stegle, Alexis Battle, Peter M. Visscher, Jian Yang, Markus Scholz, Joseph Powell, Greg Gibson, Tonu Esko, Lude Franke
Summary: Genetic variants associated with traits primarily affect complex phenotypes through regulatory mechanisms on the transcriptome. Most genes show cis-eQTL effects, while distal trans-eQTL effects have lower replication rates. However, single-cell RNA-seq data prioritize intracellular trans-eQTL effects mediated by transcription factors. Additionally, a subset of genes correlated with polygenic scores for various phenotypes may serve as potential drivers for those traits.
Article
Oncology
Sameer Mirza, Achyuth Kalluchi, Mohsin Raza, Irfana Saleem, Bhopal Mohapatra, Dhananjaya Pal, Michel M. Ouellette, Fang Qiu, Lulu Yu, Alexei Lobanov, Zhi-Ming Zheng, Ying Zhang, Mansour A. Alsaleem, Emad A. Rakha, Hamid Band, M. Jordan Rowley, Vimla Band
Summary: This study reveals a novel role of ECD in viral and cellular mRNA splicing to support HPV-driven oncogenesis. ECD interacts with high-risk HPV E6 proteins and is overexpressed in cervical and head and neck squamous cell carcinoma. Its overexpression predicts shorter survival in patients and ECD knockdown impairs oncogenic behavior in cervical cancer cells.
MOLECULAR CANCER RESEARCH
(2022)
Article
Microbiology
Lulu Yu, Zhi-Ming Zheng
Summary: This article reanalyzes a previous study on HPV16 circular RNA circE7 and finds off-target effects in the research. The experimental results show that the copy number of circE7 in CaSki cells is very low and mainly located in the cytoplasm.
Review
Microbiology
Nishi R. Sharma, Zhi-Ming Zheng
Summary: RNA granules are important for post-transcriptional gene regulation. KSHV, a DNA virus, counteracts RNA granules through the expression of ORF57 protein, allowing it to evade host antiviral immunity and ensure productive infection.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Lulu Yu, Vladimir Majerciak, Zhi-Ming Zheng
Summary: Human papillomaviruses (HPV) are a group of viruses that cause cancer, with HPV16 and HPV18 being the most common types responsible for majority of cases. The expression of their genome is regulated by alternative RNA splicing, and epigenetic modifications also play a role in HPV infections and carcinogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Multidisciplinary Sciences
Haibin Liu, Zhi-Ming Zheng
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Letter
Microbiology
Lulu Yu, Alexei Lobanov, Zhi-Ming Zheng
Article
Cell Biology
Ashish Kumar, Yuanzhi Lyu, Yuichi Yanagihashi, Chanikarn Chantarasrivong, Vladimir Majerciak, Michelle Salemi, Kang-Hsin Wang, Tomoki Inagaki, Frank Chuang, Ryan R. Davis, Clifford G. Tepper, Kazushi Nakano, Chie Izumiya, Michiko Shimoda, Ken-ichi Nakajima, Alexander Merleev, Zhi-Ming Zheng, Mel Campbell, Yoshihiro Izumiya
Summary: This study reveals the nuclear microenvironment of Kaposi sarcoma-associated herpesvirus (KSHV) and its role in regulating the latency-lytic replication switch. Viral long non-coding RNAs interact with CHD4 to control KSHV reactivation.
Correction
Biochemistry & Molecular Biology
Lulu Yu, Vladimir Majerciak, Zhi-Ming Zheng
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Vladimir Majerciak, Beatriz Alvarado-Hernandez, Alexei Lobanov, Maggie Cam, Zhi-Ming Zheng
Summary: In this report, the researchers investigated the role of RNA splicing in the regulation of KSHV gene expression. They found that approximately one-third of viral genes express spliced transcripts, many of which undergo RNA alternative splicing. They identified a subset of viral RNA splicing events that are regulated by the viral RNA-binding protein ORF57, leading to the discovery of its role in the splicing of the bicistronic ORF70-K3 RNA and production of viral thymidylate synthase ORF70 and viral E3-ubiquitin ligase K3. This regulation allows for the timely expression of these two viral proteins during the KSHV lytic cycle. The study provides new insights into KSHV biology and serves as a blueprint for studying RNA splicing in other pathogens.
Article
Chemistry, Medicinal
Lei Sun, Zhi-Ming Zheng, Chang-Sheng Shao, Zhi-Yong Zhang, Ming-Wei Li, Li Wang, Han Wang, Gen-Hai Zhao, Peng Wang
Summary: In this study, we analyzed the structures of human GLP-1, DPP-4, and GLP-1 receptors and designed new GLP-1 receptor agonists that improved stability. Molecular modeling, molecular dynamics calculations, and simulations were used to obtain possible tertiary structure models and docking results with DPP-4 and GLP-1R. The modified GLP-1RAs effectively prevented degradation by DPP-4 while maintaining their ability to bind to GLP-1R. This research provides important insights for the development of GLP-1RAs and demonstrates the application of structural biology-based protein design in drug development.
Article
Virology
Qiang Xu, Haoru Dong, Zhiyu Wang, Pei Zhang, Andreas E. E. Albers, Andreas M. M. Kaufmann, Zhi-Ming Zheng, Xu Qian
Summary: A new platform was used to genotype HPV DNA in cancer tissues of 361 gastric cancer (GC) and 89 oropharyngeal squamous cell carcinoma (OPSCC). The results showed that 10 GC and 2 OPSCC were infected with HPV16, suggesting a possible involvement of high-risk HPV in gastric carcinoma.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Environmental Sciences
Junjie Niu, Tiequan Zhang, Guang Wen, Zhiming Zheng, Yu Jia, Chin S. Tan, Tom Welackey
Summary: Evaluating the nitrogen use efficiency of animal manure is crucial for optimizing its application in profitable crop production without harming the environment. A four-year field study found that liquid manure achieved comparable corn yields to inorganic fertilizer, while solid and composted manure had minimal agronomical value. Nitrogen use efficiency indices were used to evaluate the different manures, with inorganic fertilizer performing the best followed by liquid manure.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Vladimir Majerciak, Tongqing Zhou, Michael J. Kruhlak, Zhi-Ming Zheng
Summary: In this study, the formation of stress granules (SG) induced by arsenite (ARS) was found to be topologically and mechanically linked to RNA-processing bodies (PB). Two essential PB components, GW182 and DDX6, play direct but distinguishable roles in SG biogenesis under stress. The activity of DDX6 in both PB and SG biogenesis is further modulated by its interaction with CNOT1 and 4E-T.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Virology
Beatriz Alvarado-Hernandez, Yanping Ma, Nishi R. Sharma, Vladimir Majerciak, Alexei Lobanov, Maggie Cam, Jun Zhu, Zhi-Ming Zheng
Summary: In this study, the researchers investigated the role of KSHV ORF57 in binding and regulating host noncoding RNAs, including lncRNAs, snoRNAs, and rRNAs. They found that ORF57 interacts with a subset of lncRNAs and snoRNAs to regulate their expression. Additionally, ORF57 binds and regulates rRNA modifications. The researchers also discovered that ORF57 associates with actively translating polysomes and modulates PABPC1 and Ago2 binding to polysomes.
JOURNAL OF VIROLOGY
(2022)
Article
Microbiology
Lulu Yu, Zhi-Ming Zheng
Summary: The study found that the copy number of circE7 in HPV16-positive cervical cancer cell lines is low, and its function mainly results from off-target effects on E6*I RNA.