Article
Biotechnology & Applied Microbiology
Ang Qu, Yulin Bai, Xinyi Zhang, Junjia Zeng, Fei Pu, Linni Wu, Peng Xu, Tao Zhou
Summary: In this study, the molecular mechanisms and regulation processes for the large yellow croaker's resistance to Cryptocryon irritans infection were investigated. The results showed that alternative splicing and differentially expressed isoforms play important roles in the immune response, providing insights into the immune-related roles of DAS and DEIs in the infection process of L. crocea.
MARINE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Eun Ji Lee, Seung-Jae Noh, Huiseon Choi, Min Woo Kim, Su Jin Kim, Yeon Ah Seo, Ji Eun Jeong, Inkyung Shin, Jong-Seok Kim, Jong-Kwon Choi, Dae-Yeon Cho, Suhwan Chang
Summary: This study used RNA-seq analysis to investigate the changes in splicing patterns and correlations of tissue-specific genes during primary-patient derived xenograft (PDX) tumor formation. The results revealed significant changes in splicing patterns and overall strong positive correlations between primary and PDX tumors, except for gastric cancer cases. These findings suggest that tissue specificity and splicing events may play a role in primary-PDX integrity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemical Research Methods
Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li
Summary: Alternative splicing (AS), a key pathway for transcriptional regulation, has been shown to be associated with complex diseases. Computational approaches for detecting disease-associated AS events have been developed. This review discusses the metrics used for characterizing AS events quantitatively. It also reviews and discusses three types of methods for detecting disease-associated splicing events: differential splicing analysis, aberrant splicing detection, and splicing-related network analysis. Additionally, methods for detecting genetic variants that potentially regulate splicing are described. Experimental comparisons are conducted to illustrate the performance of each method. The limitations of these methods are discussed, as well as potential ways to address them. This review aims to provide a systematic understanding of computational approaches for analyzing disease-associated splicing.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Casey S. Jacobsen, Prince Salvador, John F. Yung, Sabrina Kragness, Herra G. Mendoza, Gail Mandel, Peter A. Beal
Summary: Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosine to inosine in duplex RNA, resulting in an effective A-to-G edit. ADAR editing can lead to recoding events and alterations in RNA function. One limitation of ADAR is its preference for editing adenosines with specific neighboring nucleotides, but new strategies and approaches are being developed to overcome this.
ACS CHEMICAL BIOLOGY
(2023)
Article
Neurosciences
Paul S. Baxter, Owen Dando, Giles E. Hardingham
Summary: A single gene can produce multiple proteins through the differential splicing of exons, which can be controlled by activity-dependent calcium signaling in neurons. Specific splicing at splice-site 4 (SS4) of the Neurexin 1 gene affects postsynaptic NMDA receptor responses. Previous research reported a delayed-onset shift in splicing, but this study reveals that high K+ depolarization induces neuronal death and the observed changes in splicing are primarily driven by astrocytes rather than neurons. The findings emphasize the significance of NMDA receptor blockade when using high K+ depolarizing stimuli.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Review
Endocrinology & Metabolism
Panyisha Wu, Moya Zhang, Nicholas J. G. Webster
Summary: Alternative RNA splicing is an important biological process that has been linked to various clinical syndromes, but its applicability to common diseases is still uncertain. This review focuses on the changes in alternative RNA splicing in fatty liver disease and the role of splicing regulation in disease progression.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Carmelo Gurnari, Simona Pagliuca, Valeria Visconte
Summary: Alternative RNA splicing is an essential physiological function that plays a crucial role in cellular development. RNA splicing dysfunction has been implicated in the development of several cancers, including myeloid malignancies. Cancer cells exhibit marked gene expression alterations, including different usage of AS isoforms, potentially causing tissue-specific effects and disruptions of downstream pathways.
Review
Immunology
Jianli Zhou, Qiao Zhang, Yuzhen Zhao, Yuchen Song, Yanan Leng, Moxian Chen, Shaoming Zhou, Zhaoxia Wang
Summary: Inflammatory bowel disease (IBD) is a group of chronic diseases including Crohn's disease and ulcerative colitis, which have a global impact on both children and adults. The burden of IBD is increasing worldwide, and the costs associated with it are high. The pathogenesis of IBD is still unclear, but is believed to be related to environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. This article reviews the research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Oncology
Anthony J. Murphy, Alex H. Li, Peichao Li, Hong Sun
Summary: Alternative splicing plays a crucial role in diversifying the proteome and has significant implications in cancer development. Recent studies have highlighted the important roles of SR proteins in cancer progression. Understanding the spliceosome and its relationship to cancer has opened up new opportunities for therapeutic interventions based on alternative splicing.
FRONTIERS IN ONCOLOGY
(2022)
Article
Genetics & Heredity
Qi Liu, Leiming Fang, Chengjun Wu
Summary: Alternative splicing of pre-mRNA is a key mechanism for increasing protein complexity, leading to diversity of transcriptomes and proteomes in a tissue-specific manner. Changes and errors in splicing regulation caused by splicing factors are closely related to various diseases. Understanding cellular factors that mediate alternative splicing regulation is a potential avenue for developing specific drugs targeting the dynamic RNA splicing process.
Article
Cell Biology
Zhe Liu, Wei Wang, Xinru Li, Xiujuan Zhao, Hongyu Zhao, Wuritu Yang, Yongchun Zuo, Lu Cai, Yongqiang Xing
Summary: Alternative splicing plays an important role in zebrafish embryo development, especially during the maternal-to-zygotic transition process where it is highly abundant and dynamic. Splicing factors are expressed with developmental stage specificity, with a higher expression during the maternal-to-zygotic transition. The inclusion level of alternative splicing events performs well in cluster analysis and can be used as a novel parameter.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Oncology
Jiawei Ouyang, Yijie Zhang, Fang Xiong, Shanshan Zhang, Zhaojian Gong, Qijia Yan, Yi He, Fang Wei, Wenling Zhang, Ming Zhou, Bo Xiang, Fuyan Wang, Xiaoling Li, Yong Li, Guiyuan Li, Zhaoyang Zeng, Can Guo, Wei Xiong
Summary: This article introduces the definition of alternative splicing in eukaryotes and its importance in cancer development. Alternative splicing is a transcription process that allows coding genes to be translated into multiple proteins with different functions. Alterations in splicing mechanisms may lead to changes in the splicing patterns of cancer-related genes.
AMERICAN JOURNAL OF CANCER RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Yuanjiao Zhang, Jinjun Qian, Chunyan Gu, Ye Yang
Summary: The study systematically describes the abnormal regulation and functions of alternative splicing in tumors, as well as introduces therapeutic strategies targeting splicing catalysis and regulatory proteins. Further research is needed to fully understand the association between alternative splicing and cancer.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2021)
Article
Evolutionary Biology
Laura Martinez-Gomez, Daniel Cerdan-Velez, Federico Abascal, Michael L. Tress
Summary: Tandem duplicated exon substitution events are rare but highly important alternative splicing events. The isoforms produced from these events are often highly expressed and have more pathogenic mutations compared to other splice events. The important structural and functional residues in the homologous regions are conserved, with most changes being conservative. The isoforms produced from these events are tissue-specific, particularly in nervous and cardiac tissues, and are enriched in functional terms related to structures in the brain and skeletal muscle. Additionally, there is evidence of convergent evolution of these events in vertebrates, arthropods, and nematodes.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Feiyang Zhao, Yubin Yan, Yaxi Wang, Yuan Liu, Ruolin Yang
Summary: The study reveals the prevalence of highly splicing complex exons in mammals and their correlation with gene features. The splicing complexity of exons can be moderately predicted using machine learning and deep learning methods. Both developmentally regulated and non-developmentally regulated exons show dynamic splicing complexity during organ development.