Article
Biochemistry & Molecular Biology
Zakaria Louadi, Kevin Yuan, Alexander Gress, Olga Tsoy, Olga Kalinina, Jan Baumbach, Tim Kacprowski, Markus List
Summary: Alternative splicing plays a crucial role in regulating the functional diversity of the proteome, but its isoform-specific effects on protein-protein interactions are often overlooked. By integrating various interaction information, researchers have developed a user-friendly database called DIGGER to study mechanistic consequences of alternative splicing, providing a valuable resource for exploring the functional role of individual exons on a network level.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Ting-Lin Pang, Zhan Ding, Shao-Bo Liang, Liang Li, Bei Zhang, Yu Zhang, Yu-Jie Fan, Yong-Zhen Xu
Summary: RNA splicing is critical in gene expression regulation, with microexons (especially those shorter than 8 nt) being relatively understudied in many organisms. Analysis of Drosophila mRNA-seq data with ce-TopHat identified 465 new microexons, and differentially alternatively spliced microexons were investigated between different Drosophila tissues and genders.
FRONTIERS IN GENETICS
(2021)
Article
Developmental Biology
Cansu Akkaya, Dila Atak, Altug Kamacioglu, Busra Aytul Akarlar, Gokhan Guner, Efil Bayam, Ali Cihan Taskin, Nurhan Ozlu, Gulayse Ince-Dunn
Summary: KIF2A is essential for dendritic arborization and radial migration of cortical neurons during brain development. Three Kif2a isoforms were studied, with only two supporting neuronal migration. A KIF2A mutation causing brain malformations led to changes in its interactome, including depletion of mitochondrial proteins.
Article
Cell Biology
Daniel Alejandro Careno, Constanza Helena Assaf, Eline Dieuwerke Catharina Eggermont, Micaela Canelo, Pablo Diego Cerdan, Marcelo Javier Yanovsky
Summary: Light serves as the main source of energy and an important environmental signal for plants. It regulates gene expression, splicing, and alternative splicing processes. Two main pathways, photosynthesis-related signal and photosensory proteins, have been proposed to link light sensing with splicing machinery. The relative contribution of each pathway and the overlap of their targets in terms of splicing regulation depend on the developmental stage of plants.
Article
Genetics & Heredity
Zhibing Dai, Yachao Sun, Maierdanjiang Maihemuti, Renbing Jiang
Summary: This study conducted a genome-wide analysis to investigate the alternative splicing events associated with the development of osteosarcoma. The results showed that alternative splicing is closely related to the immune response process and involves specific immune cell types. By establishing a co-regulatory network, RNA-binding proteins that regulate alternative splicing and are associated with osteosarcoma immune regulation were identified, providing potential molecular targets for osteosarcoma immunotherapy.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Feifei Zhang, Hui Wang, Jiang Yu, Xueqing Yao, Shibin Yang, Weidong Li, Lijun Xu, Liang Zhao
Summary: The study found that CRNDE plays a key role in gastric cancer chemotherapy by regulating autophagy and alternative splicing events.
Article
Biotechnology & Applied Microbiology
Baohua Tan, Jiekang Zeng, Fanming Meng, Shanshan Wang, Liyao Xiao, Xinming Zhao, Linjun Hong, Enqin Zheng, Zhenfang Wu, Zicong Li, Ting Gu
Summary: This study suggests that m6A modification plays an important role in mediating the phenotypic differences between oxidative and glycolytic muscles through the regulation of alternative splicing (AS), providing novel insights into the mechanisms underlying muscle fiber conversion.
Article
Cell Biology
Riho Komuro, Yuka Honda, Motoaki Yanaizu, Masami Nagahama, Yoshihiro Kino
Summary: Genetic variations of CD33, specifically the rs12459419 polymorphism on exon 2, affect its alternative splicing and have been associated with the risk of Alzheimer's disease. The minor allele promotes skipping of exon 2, resulting in a shorter CD33 isoform lacking the ligand-binding domain and reduced suppressive signaling on microglial activity. HNRNPA1 was found to promote exon 2 skipping, but simultaneous knockdown of HNRNPA1, HNRNPA2B1, and HNRNPA3 increased exon 2 inclusion, suggesting functional redundancy among these proteins.
Article
Plant Sciences
Tingyu Ma, Han Gao, Dong Zhang, Wei Sun, Qinggang Yin, Lan Wu, Tianyuan Zhang, Zhichao Xu, Jianhe Wei, Yanyan Su, Yuhua Shi, Dandan Ding, Ling Yuan, Gangqiang Dong, Liang Leng, Li Xiang, Shilin Chen
Summary: Artemisinin is the most effective ingredient in treating malaria, making it important to study the genetic regulation of Artemisia annua. This study found that alternative splicing in the artemisinin biosynthetic pathway is influenced by light, potentially regulating sesquiterpenoid biosynthesis. The analysis provided valuable insights into the complexity of transcriptome and proteome in plant alternative splicing.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Kofi Amoah, Yun-Hua Esther Hsiao, Jae Hoon Bahn, Yiwei Sun, Christina Burghard, Boon Xin Tan, Ei-Wen Yang, Xinshu Xiao
Summary: Alternative splicing is a RNA processing mechanism that affects most genes in human, and can be modulated by genetic variants. Utilizing GTEx data, the study of genetically modulated alternative splicing (GMAS) reveals that GMAS events are shared more frequently across tissues and individuals than expected by chance, indicating a genetically driven nature.
Article
Cardiac & Cardiovascular Systems
Carlos Marti-Gomez, Javier Larrasa-Alonso, Marina Lopez-Olaneta, Maria Villalba-Orero, Pablo Garcia-Pavia, Fatima Sanchez-Cabo, Enrique Lara-Pezzi
Summary: This study investigates the role of alternative splicing (AS) in heart disease and its relationship with heart development. It reveals the complex regulatory mechanisms and potential protein-protein interaction changes associated with AS changes, particularly in heart disease. The over-expression of PTBP1 is found to play a central role in regulating AS and is associated with cardiac hypertrophy and diastolic dysfunction.
JOURNAL OF CARDIOVASCULAR TRANSLATIONAL RESEARCH
(2022)
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)
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)
Review
Neurosciences
Roman Sloutsky, Margaret M. Stratton
Summary: Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a crucial regulator in the post-synapse during long-term potentiation, encoded by four genes in humans with alternative splicing leading to a diversity of proteins. Advances in sequencing technologies have led to the discovery of new CaMKII transcripts and suggest the adoption of a new naming scheme for CaMKII variants to better understand their biological implications.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2021)
Review
Plant Sciences
Praveen Kumar Kathare, Enamul Huq
Summary: The article summarizes the role of phytochromes in regulating plant growth and development, particularly in the regulation of pre-mRNA splicing process.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Genetics & Heredity
Celine Fernando, Agnes Audibert, Francoise Simon, Jamal Tazi, Francois Juge
Article
Virology
Noelie Campos, Renier Myburgh, Aude Garcel, Audrey Vautrin, Laure Lapasset, Erika Schlaepfer Nadal, Florence Mahuteau-Betzer, Romain Najman, Pauline Fornarelli, Katjana Tantale, Eugenia Basyuk, Martial Seveno, Julian P. Venables, Bernard Pau, Edouard Bertrand, Mark A. Wainberg, Roberto F. Speck, Didier Scherrer, Jamal Tazi
Article
Genetics & Heredity
Celine Fernando, Agnes Audibert, Francoise Simon, Jamal Tazi, Francois Juge
Article
Biochemistry & Molecular Biology
Maia Lanfranco, Rebecca Cacciottolo, Rebecca M. Borg, Neville Vassallo, Francois Juge, Remy Bordonne, Ruben J. Cauchi
Article
Biochemistry & Molecular Biology
Marine Pons, Laetitia Miguel, Camille Miel, Tracey Avequin, Francois Juge, Thierry Frebourg, Dominique Campion, Magalie Lecourtois
HUMAN MOLECULAR GENETICS
(2017)
Article
Biochemistry & Molecular Biology
Isabel C. Lopez-Mejia, Marion de Toledo, Carine Chavey, Laure Lapasset, Patricia Cavelier, Celia Lopez-Herrera, Karim Chebli, Philippe Fort, Guillaume Beranger, Lluis Fajas, Ez Z. Amri, Francois Casas, Jamal Tazi
Article
Multidisciplinary Sciences
Sophie Martin, Jamal Tazi
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2014)
Editorial Material
Cell Biology
Helene Tourriere, Jamal Tazi
JOURNAL OF CELL BIOLOGY
(2019)
Article
Cell Biology
Anne Ramat, Maria-Rosa Garcia-Silva, Camille Jahan, Rima Nait-Saidi, Jeremy Dufourt, Celine Garret, Aymeric Chartier, Julie Cremaschi, Vipul Patel, Mathilde Decourcelle, Amandine Bastide, Francois Juge, Martine Simonelig
Article
Biochemistry & Molecular Biology
Abdelhamid Mahdi Laaref, Laurent Manchon, Yacine Bareche, Laure Lapasset, Jamal Tazi
Article
Multidisciplinary Sciences
Bruno Mugat, Simon Nicot, Carolina Varela-Chavez, Christophe Jourdan, Kaoru Sato, Eugenia Basyuk, Francois Juge, Mikiko C. Siomi, Alain Pelisson, Severine Chambeyron
NATURE COMMUNICATIONS
(2020)
Review
Pharmacology & Pharmacy
Jamal Tazi, Christina Begon-Pescia, Noelie Campos, Cecile Apolit, Aude Garcel, Didier Scherrer
Summary: Inflammatory diseases are believed to result from dysregulated inflammatory responses to environmental factors on susceptible genetic backgrounds. MiRNAs, such as miR-124, are endogenous, small noncoding RNAs that play a role in regulating gene expression involved in inflammation. ABX464, a small quinoline compound, has shown promising efficacy in ulcerative colitis by upregulating miR-124 and restoring physiological pathways lost in inflammatory diseases.
DRUG DISCOVERY TODAY
(2021)
Article
Biochemistry & Molecular Biology
Diwas Srivastava, Marion de Toledo, Laurent Manchon, Jamal Tazi, Francois Juge
Summary: The Hippo signaling pathway regulates organ growth by controlling the activity of the transcription coactivator Yorkie (Yki) in Drosophila and its homolog YAP in mammals. Alternative splicing of the Yki gene is modulated by the splicing factor B52, leading to differences in protein composition and developmental instability. This study highlights the importance of alternative splicing in modulating the Hippo pathway and maintaining developmental robustness.