Article
Immunology
Meng Zhao, Jingxin Zhou, Yihu Tang, Mingzhu Liu, Yawei Dai, Hui Xie, Zihao Wang, Liang Chen, Yanhu Wu
Summary: This study investigates the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of mitral valve prolapse (MVP). RNA-seq was performed on peripheral blood mononuclear cells (PBMCs) from MVP patients and healthy individuals. Dysregulated RBPs and their associated RASEs were found to play regulatory roles in MVP development.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Agronomy
Xiaojiao Hu, Hongwu Wang, Kun Li, Xiaogang Liu, Zhifang Liu, Yujin Wu, Shuqiang Li, Changling Huang
Summary: The study reveals a large number of significant differential alternative splicing events in the maize hybrid ZD808 compared to its parents, with NG5-dominant events playing a prevalent role and mainly involved in regulating genes associated with carbon/nitrogen metabolism and cell division processes.
Review
Genetics & Heredity
M. Brandon Titus, Adeline W. Chang, Eugenia C. Olesnicky
Summary: Alternative splicing is a fundamental mechanism of eukaryotic RNA regulation that increases complexity in transcriptomes and proteomes. Understanding aberrant splicing has shed light on developmental and neurodegenerative diseases, leading to innovative therapeutic treatments. Research on distinct protein-coding spliceforms and the use of noncoding exons in alternative splicing can provide insights into physiological roles and specific functions of gene spliceforms.
FRONTIERS IN GENETICS
(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
Genetics & Heredity
Shiyong Wu, Shibiao Liu, Ningheng Chen, Chuang Zhang, Hairong Zhang, Xueli Guo
Summary: The study utilized bioinformatics methods to investigate immune-related genes and immune-RAS in AAA. The findings suggest that immune-related genes, immune-RAS, and splicing factors play significant roles in AAA.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Zeyuan Yang, Yijie He, Yongheng Wang, Lin Huang, Yaqin Tang, Yue He, Yihan Chen, Zhijie Han
Summary: This study comprehensively analyzed the impact of DNA methylation, gene expression, and alternative splicing on glioma, and identified key genes associated with prognosis of glioma. These findings contribute to a better understanding of the pathogenesis of glioma.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Jing Song, Jia Liu, Dekang Lv, Xuan Meng, Xiaodong Li
Summary: This study identified survival-associated AS signatures in Lung Adenocarcinoma (LUAD) and established a new combined prognostic model with strong predictive properties. The research also revealed a splicing network between AS and SFs, as well as a possible mechanism for tumors to evade immune recognition by decreasing expression of antigen presentation genes. Additionally, several small-molecule drugs were provided as potential inhibitors of LUAD, with NVP-AUY922 showing promising results in prolonging patient survival.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Anjan Hazra, Pradosh Mahadani
Summary: This study reveals the genome-wide landscape of alternative splicing (AS) and its functional significance in Orchids under different stress conditions. The results demonstrate the widespread existence of AS in Orchids and its important roles in cold acclimation and pathogen stress. Alternative acceptor sites and intron retentions are the most common types of AS events. AS-affected genes are primarily involved in cellular metabolism and RNA processing. Additionally, AS can regulate Orchids' response to various biotic and abiotic stresses.
SOUTH AFRICAN JOURNAL OF BOTANY
(2022)
Article
Genetics & Heredity
Kyubin Lee, Doyeong Yu, Daejin Hyung, Soo Young Cho, Charny Park
Summary: In this study, a novel application called ASpediaFI was developed to systematically identify differential alternative splicing (AS) events, co-regulated genes, and pathways. ASpediaFI exhibited strong performance in both simulated and public datasets, demonstrating its ability to effectively detect biologically relevant candidate genes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Xuena Huang, Hanxi Li, Aibin Zhan
Summary: This study investigates the alternative splicing (AS) response patterns in closely related invasive ascidians, Ciona robusta and Ciona savignyi, under environmental changes. It reveals the factors influencing AS variation and uncovers species-specific and environmentally dependent AS responses to environmental challenges.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Xin Qi, Hongchang Gu, Lujiang Qu
Summary: This study investigated the inheritance patterns of alternative splicing in chickens through a reciprocal crossing experiment between White Leghorn and Cornish Game chicken breeds. Significant differences in alternative splicing events were observed between the two breeds in brain, muscle, and liver tissues, highlighting tissue and strain specificity. The study also revealed that a substantial portion of alternative splicing genes show conserved patterns in parental strains and hybrid crosses across all three tissues.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Jie Xiao, Wen-Xiong Wang
Summary: The transcript variant and alternative splicing play crucial roles in zebrafish development, regulating stage-specific functions by adjusting gene expression and generating diverse protein isoforms.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biology
Showkat Ahmad Ganie, Anireddy S. N. Reddy
Summary: When facing environmental stresses, alternative splicing (AS) plays a crucial role in rice by rapidly regulating gene expression to help the plant adapt to various pressures. Studies have shown that AS is important for rice growth and development, especially under stress conditions. Understanding the impact of AS on rice and its pathogens can provide valuable insights for developing stress-resistant rice varieties in the future.
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)
Review
Cell Biology
Ning Wang, Yue Hu, Zefeng Wang
Summary: Eukaryotic gene expression is tightly regulated at multiple levels, including alternative splicing, which generates multiple mRNA isoforms from a single gene. Epigenetic modifications play crucial roles in the regulation of alternative splicing by affecting transcription, splicing factor recruitment, and splicing factor expression/activity. Dysregulation of epigenetics and splicing is common in cancer and can have functional consequences. Understanding the complex regulation of gene expression layers can provide new insights into modulating disease-related splicing dysregulation.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Biotechnology & Applied Microbiology
Marianne Stage, Anita Wichmann, Mette Jorgensen, Natalia Ivonne Vera-Jimenez, Malue Wielje, Dennis Sandris Nielsen, Albin Sandelin, Yun Chen, Adam Baker
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Xueyuan Leng, Maxim Iyanov, Peter Kindgren, Indranil Malik, Axel Thieffry, Peter Brodersen, Albin Sandelin, Craig D. Kaplan, Sebastian Marquardt
Article
Cell Biology
Guifen Wu, Manfred Schmid, Leonor Rib, Patrik Polak, Nicola Meola, Albin Sandelin, Torben Heick Jensen
Article
Oncology
Deobrat Dixit, Briana C. Prager, Ryan C. Gimple, Hui Xian Poh, Yang Wang, Qiulian Wu, Zhixin Qiu, Reilly L. Kidwell, Leo J. Y. Kim, Qi Xie, Kristoffer Vitting-Seerup, Shruti Bhargava, Zhen Dong, Li Jiang, Zhe Zhu, Petra Hamerlik, Samie R. Jaffrey, Jing Crystal Zhao, Xiuxing Wang, Jeremy N. Rich
Summary: Research reveals that m6A mRNA modifications are upregulated in glioblastoma stem cells, with the key m6A reader YTHDF2 stabilizing important transcripts such as MYC. Targeting the YTHDF2-MYC-IGFBP3 axis could potentially be a novel therapeutic approach for glioblastoma. Epitranscriptomics have the potential to reveal specific vulnerabilities in cancer cells that can be targeted for treatment.
Article
Cell Biology
Camilla Bjornbak Holst, Henriette Pedersen, Elisabeth Anne Adanma Obara, Kristoffer Vitting-Seerup, Kamilla Ellermann Jensen, Jane Skjoth-Rasmussen, Eva Lobner Lund, Hans Skovgaard Poulsen, Julia Sidenius Johansen, Petra Hamerlik
Summary: In the study, the challenges in treating GBM patients were explored, including the frustrations brought by anti-angiogenic agents and immunotherapy, the historical trajectory of bevacizumab as a treatment modality, and the role of dual targeting strategies in therapy. The study emphasizes that pursuing pleiotropic targets and leaning toward multitarget strategies may be key to more effective therapeutic intervention in GBM.
Article
Biochemical Research Methods
Maxim Ivanov, Albin Sandelin, Sebastian Marquardt
Summary: The study developed an automated transcriptome annotation pipeline, TranscriptomeReconstructoR, which integrates features from different datasets to achieve more accurate and comprehensive gene model recall. By supplementing existing models with new RNA-seq data, the package has the potential to improve the quality of plant and yeast genome research.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Mathys Grapotte, Manu Saraswat, Chloe Bessiere, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyamas, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C. Frith, Clement Chatelain, Piero Carninci, Michiel J. L. de Hoom, Wyeth W. Wasserman, Laurent Brehelin, Charles-Henri Lecellieree
Summary: The FANTOM5 consortium used CAGE technology to map transcription start sites, finding that a large portion of non-coding transcription initiates at microsatellites. They developed Cap Trap RNA-seq to confirm this transcription, and trained deep learning models to predict CAGE signal at STRs with high accuracy. These models revealed the importance of STR surrounding sequences for distinguishing STR classes and predicting transcription initiation levels.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Yi Chieh Lim, Kamilla E. Jensen, Diana Aguilar-Morante, Lina Vardouli, Kristoffer Vitting-Seerup, Ryan C. Gimple, Qiulian Wu, Henriette Pedersen, Kirstine J. Elbaek, Irina Gromova, Robert Ihnatko, Bjarne W. Kristensen, Jeanette K. Petersen, Jane Skjoth-Rasmussen, William Flavahan, Jeremy N. Rich, Petra Hamerlik
Summary: In this study, we identified PFKM as a driver of bevacizumab resistance in GBM. Cytosolic PFKM interacted with KIF11 to promote tumor invasion, while nuclear PFKM safeguarded genomic stability of tumor cells through interaction with NBS1. Based on these findings, we explored the potential of the drug bupivacaine to target PFKM and found that it enhanced the efficacy of bevacizumab in preclinical GBM models in vivo.
Article
Cell Biology
Matilda Rehn, Anne Wenzel, Anne-Katrine Frank, Mikkel Bruhn Schuster, Sachin Pundhir, Nanna Jorgensen, Kristoffer Vitting-Seerup, Ying Ge, Johan Jendholm, Magali Michaut, Erwin M. Schoof, Tanja Lyholm Jensen, Nicolas Rapin, Russell T. Sapio, Kasper Langebjerg Andersen, Anders H. Lund, Michele Solimena, Martin Holzenberger, Dimitri G. Pestov, Bo Torben Porse
Summary: Ribosomopathies are a range of disorders that affect protein synthesis and primarily impact hematopoietic stem cells and erythroid development. This study demonstrates that the deletion of poly-pyrimidine-tract-binding protein 1 (PTBP1) in the hematopoietic compartment leads to a condition resembling ribosomopathy. The loss of PTBP1 results in reduced HSC self-renewal, erythroid differentiation, and protein synthesis, along with defects in splicing and ribosome biogenesis.
Editorial Material
Biochemistry & Molecular Biology
Abdullah Kahraman, Marija Buljan, Kristoffer Vitting-Seerup
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Developmental Biology
Jennifer N. Chousal, Abhishek Sohni, Kristoffer Vitting-Seerup, Kyucheol Cho, Matthew Kim, Kun Tan, Bo Porse, Miles F. Wilkinson, Heidi Cook-Andersen
Summary: Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway. In mouse blastocysts, the core NMD factor UPF2 is required for expansion of epiblast cells, indicating the essential role of NMD in embryonic cell proliferation and survival.
Article
Anatomy & Morphology
Camilla Bjornbak Holst, Christian Beltoft Brochner, Kristoffer Vitting-Seerup, Kjeld Mollgard
Summary: Outer radial glial cells (oRGs) give rise to neurons and glial cells and contribute to cell migration and expansion in developing neocortex. HOPX has been described as a marker of oRGs and possible actor in glioblastomas. Recent years' evidence points to spatiotemporal differences in brain development which may have implications for the classification of cell types in the central nervous system and understanding of a range of neurological diseases.
JOURNAL OF ANATOMY
(2023)
Article
Biology
Soren Helweg Dam, Lars Ronn Olsen, Kristoffer Vitting-Seerup
Summary: This study used pairedGSEA to analyze a large number of RNA-seq datasets and found that alternative splicing contributes to 48.1% of the biological signal in expression analyses on average. Both expression and splicing convey shared and distinct biological signals. These findings establish alternative splicing as a major regulator of the human condition and suggest that most contemporary RNA-seq studies likely miss out on critical biological insights.
Article
Genetics & Heredity
Kristoffer Vitting-Seerup
Summary: Protein domains exist as multiple variants, termed domain isotypes, which are used in different cells, tissues, and diseases and have different three-dimensional structures. Contrary to the current view, domain isotypes can modulate or abolish the functionality of protein domains. This has significant implications for laboratory workflows.
NAR GENOMICS AND BIOINFORMATICS
(2023)
