Article
Microbiology
Wei Shi, Jun Yang, Deng Chen, Changfa Yin, Huixia Zhang, Xiaozhou Xu, Xiao Pan, Ruijin Wang, Liwang Fei, Mengfei Li, Linlu Qi, Vijai Bhadauria, Junfeng Liu, You-Liang Peng
Summary: This study reveals the unique mechanisms by which the fungal conserved SR protein MoSrp1 regulates alternative pre-mRNA splicing in the model plant fungal pathogen Magnaporthe oryzae. MoSrp1 enhances and suppresses alternative splicing by binding to the GUAG consensus in target pre-mRNAs. The GUAG consensus itself enhances and suppresses intron splicing efficiency, which is important for mycelial growth, conidiation, and virulence. MoSrp1 is SUMOylated for nuclear localization and enhancing GUAG binding capacity. The N-terminal RNA recognition domain of MoSrp1 interacts with a splicing factor and two components of the exon-joining complex and is required for fungal growth, development, and virulence.
Review
Multidisciplinary Sciences
Jiancheng Xue, Tie Ma, Xiaowen Zhang
Summary: The dysregulation of alternative splicing in cancer is commonly observed and serves as a crucial indicator for cancer progression and therapy. Transformer 2 (TRA2), a nuclear RNA binding protein, consisting of TRA2A and TRA2B, has been found to be dysregulated in various types of tumors. It modulates the proliferation, migration, invasion, and chemotherapy resistance of cancer cells by altering the alternative splicing of cancer-related genes. This review focuses on the role of TRA2 in tumorigenesis and metastasis, and discusses the potential molecular mechanisms by which TRA2 influences these processes through controlling alternative splicing. We propose that TRA2A is a novel biomarker and therapeutic target for cancer progression and therapy.
Article
Biochemical Research Methods
Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchene
Summary: This article introduces a new pipeline for designing searchable databases on the 2D and 3D structures of protein-bound nucleic acids (NA), selecting context-specific NA structures, and creating corresponding fragment libraries. The strength of this pipeline lies in its modularity, allowing it to be adapted to various specific modeling problems.
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
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
Cell Biology
Lydia M. Castelli, Ya-Hui Lin, Alvaro Sanchez-Martinez, Aytac Gul, Kamallia Mohd Imran, Adrian Higginbottom, Santosh Kumar Upadhyay, Nora M. Markus, Raquel Rua Martins, Johnathan Cooper-Knock, Claire Montmasson, Rebecca Cohen, Amy Walton, Claudia S. Bauer, Kurt J. De Vos, Richard J. Mead, Mimoun Azzouz, Cyril Dominguez, Laura Ferraiuolo, Pamela J. Shaw, Alexander J. Whitworth, Guillaume M. Hautbergue
Summary: Hexanucleotide repeat expansions in C9ORF72 are a common genetic cause of familial ALS and FTD. These expansions result in the translation of neurotoxic DPRs that contribute to neurodegeneration. A cell-penetrant peptide was found to block the export and translation of C9ORF72-repeat transcripts and toxic DPRs, leading to improved survival of ALS motor neurons and decreased DPR expression in animal models. Disrupting DPR production may be a potential strategy to ameliorate neurodegeneration in ALS/FTD.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Biotechnology & Applied Microbiology
Jinding Liu, Kun Lang, Suxu Tan, Wencai Jie, Yihua Zhu, Shiqing Huang, Wen Huang
Summary: LivestockExp is a web-based database server for exploring gene expression and alternative splicing, containing a large number of livestock animals and RNA-seq samples. It provides diverse analysis modules and visualization tools, serving as a valuable data resource and analysis platform.
Article
Multidisciplinary Sciences
Tebbe de Vries, William Martelly, Sebastien Campagne, Kevin Sabath, Chris P. Sarnowski, Jason Wong, Alexander Leitner, Stefanie Jonas, Shalini Sharma, Frederic H. -T. Allain
Summary: This study determined the 3D structure of the complex between SF3A1-UBL and U1-SL4 RNA and revealed the sequence-specific recognition of U1-SL4 by SF3A1-UBL. The results expand our understanding of RNA binding domains and demonstrate the specific binding capacity of RGG/RG motifs to RNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
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
Multidisciplinary Sciences
Yang Pan, John W. Phillips, Beatrice D. Zhang, Miyako Noguchi, Eric Kutschera, Jami McLaughlin, Pavlo A. Nesterenko, Zhiyuan Mao, Nathanael J. Bangayan, Robert Wang, Wendy Tran, Harry T. Yang, Yuanyuan Wang, Yang Xu, Matthew B. Obusan, Donghui Cheng, Alex H. Lee, Kathryn E. Kadash-Edmondson, Ameya Champhekar, Cristina Puig-Saus, Antoni Ribas, Robert M. Prins, Christopher S. Seet, Gay M. Crooks, Owen N. Witte, Yi Xing
Summary: This study describes a computational platform called IRIS that can discover tumor antigens derived from alternative splicing, providing potential targets for TCR and CAR-T immunotherapies. Through the analysis of transcriptomics and immuno-peptidomics data, the study demonstrates that the predicted targets by IRIS can bind with HLA molecules. The study illustrates the contribution of alternative splicing to the repertoire of tumor antigens and demonstrates the utility of IRIS in discovering AS-derived antigens and expanding cancer immunotherapies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Cecile Bousquet-Antonelli
Summary: RNA binding proteins play important roles in organism development by controlling mRNA fate and expression. The LARP6 subfamily has a unique evolutionary history, with studies on their cellular and molecular functions contributing to understanding of their roles.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Biochemistry & Molecular Biology
Caterina Ciani, Anna Perez-Rafols, Isabelle Bonomo, Mariachiara Micaelli, Alfonso Esposito, Chiara Zucal, Romina Belli, Vito Giuseppe D'Agostino, Irene Bianconi, Vito Calderone, Linda Cerofolini, Orietta Massidda, Michael Bernard Whalen, Marco Fragai, Alessandro Provenzani
Summary: This study identified an RNA-binding protein, AB-Elavl, in the Gram-negative pathogen Acinetobacter baumannii. The protein contains a single RNA Recognition Motif (RRM) and exhibits structural similarities to the human HuR protein. Despite some differences in binding specificity and affinity, AB-Elavl can bind to AU-rich regions similar to HuR. This finding expands our understanding of RNA-binding proteins in A. baumannii and their potential role in antibiotic resistance.
Article
Oncology
Qi Wen Chen, Qian Qian Cai, Ying Yang, Shu Dong, Yuan Yuan Liu, Zhong Yi Chen, Chun Lan Kang, Bing Qi, Yi Wei Dong, Wei Wu, Li Ping Zhuang, Ye Hua Shen, Zhi Qiang Meng, Xing Zhong Wu
Summary: This study reveals the important role and mechanism of long non-coding RNA BC in promoting tumor metastasis and influencing clinical prognosis of lung adenocarcinoma (LUAD). BC promotes growth, invasion, metastasis, and resistance to EGFR-targeted therapies in lung cancer by forming a splicing complex with nucleolin and hnRNPK. High expression of BC is associated with clinical progress and poor survival in LUAD.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
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)
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)
Review
Urology & Nephrology
Jennifer Munkley, Ian G. Mills, David J. Elliott
NATURE REVIEWS UROLOGY
(2016)
Article
Biochemistry & Molecular Biology
Marina Danilenko, Caroline Dalgliesh, Vittoria Pagliarini, Chiara Naro, Ingrid Ehrmann, Mikael Feracci, Mahsa Kheirollahi-Chadegani, Alison Tyson-Capper, Gavin J. Clowry, Philippe Fort, Cyril Dominguez, Claudio Sette, David J. Elliott
NUCLEIC ACIDS RESEARCH
(2017)
Article
Cell & Tissue Engineering
Irina Neganova, Evgenija Shmeleva, Jennifer Munkley, Valeria Chichagova, George Anyfantis, Rhys Anderson, Joao Passos, David J. Elliott, Lyle Armstrong, Majlinda Lako
Article
Multidisciplinary Sciences
Mikael Feracci, Jaelle N. Foot, Sushma N. Grellscheid, Marina Danilenko, Ralf Stehle, Oksana Gonchar, Hyun-Seo Kang, Caroline Dalgliesh, N. Helge Meyer, Yilei Liu, Albert Lahat, Michael Sattler, Ian C. Eperon, David J. Elliott, Cyril Dominguez
NATURE COMMUNICATIONS
(2016)
Article
Oncology
Jennifer Munkley, David J. Elliott
Article
Cell Biology
Ingrid Ehrmann, Matthew R. Gazzara, Vittoria Pagliarini, Caroline Dalgliesh, Mahsa Kheirollahi-Chadegani, Yaobo Xu, Eleonora Cesari, Marina Danilenko, Marie Maclennan, Kate Lowdon, Tanja Vogel, Piia Keskivali-Bond, Sara Wells, Heather Cater, Philippe Fort, Mauro Santibanez-Koref, Silvia Middei, Claudio Sette, Gavin J. Clowry, Yoseph Barash, Mark O. Cunningham, David J. Elliott
Article
Medicine, General & Internal
Jennifer Munkley, Daniel Vodak, Karen E. Livermore, Katherine James, Brian T. Wilson, Bridget Knight, Paul McCullagh, John Mcgrath, Malcolm Crundwell, Lorna W. Harries, Hing Y. Leung, Craig N. Robson, Ian G. Mills, Prabhakar Rajan, David J. Elliott
Article
Biochemical Research Methods
Monique Zangarini, Neil Rajan, Marina Danilenko, Philip Berry, Silvio Traversa, Gareth J. Veal
Article
Dermatology
Marina Danilenko, Elaine Stamp, Deborah D. Stocken, Akhtar Husain, Monique Zangarini, Amy Cranston, Robert Stones, Naomi Sinclair, Kirsty Hodgson, Susan A. Bowett, David Roblin, Silvio Traversa, Ruth Plummer, Gareth Veal, James A. A. Langtry, Alan Ashworth, John Burn, Neil Rajan
Letter
Dermatology
M. Danilenko, K. Hodgson, R. Stones, A. Husain, M. Zangarini, G. Veal, N. Rajan
BRITISH JOURNAL OF DERMATOLOGY
(2019)
Article
Biochemistry & Molecular Biology
David J. Elliott, Caroline Dalgliesh, Gerald Hysenaj, Ingrid Ehrmann
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2019)
Article
Clinical Neurology
D. Hicks, G. Rafiee, E. C. Schwalbe, C. Howell, J. C. Lindsey, R. M. Hill, A. J. Smith, P. Adidharma, C. Steel, S. Richardson, L. Pease, M. Danilenko, S. Crosier, A. Joshi, S. B. Wharton, T. S. Jacques, B. Pizer, A. Michalski, D. Williamson, S. Bailey, S. C. Clifford
Summary: Through characterizing the molecular landscape of iMB, we identified subgroups and proposed personalized, risk-adapted therapies for better outcomes.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2021)
Review
Pharmacology & Pharmacy
Marina Danilenko, Steven C. Clifford, Edward C. Schwalbe
Summary: Medulloblastoma is the most common malignant CNS tumor in children, with survivors facing lifelong late-effects from intensive treatments. Risk-stratified treatments based on better understanding of biomarkers have improved patient survival. Comprehensive understanding of disease heterogeneity within and between tumors has potential for novel therapies.
PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Clinical Neurology
Marina Danilenko, Masood Zaka, Claire Keeling, Stephen Crosier, Stephanie Lyman, Martina Finetti, Daniel Williamson, Rafiqul Hussain, Jonathan Coxhead, Peixun Zhou, Rebecca M. Hill, Debbie Hicks, Vikki Rand, Abhijit Joshi, Edward C. Schwalbe, Simon Bailey, Steven C. Clifford
Summary: We used single-cell whole-genome sequencing to reconstruct the evolutionary trajectory of medulloblastoma, the most common childhood brain malignancy. The different molecular sub-classes and clinical risk groups showed varying levels of clonal diversity and evolutionary patterns. Early-stage chromosomal aberrations and gene mutations can be used as biomarkers for early disease detection. Novel events that occur later and/or sub-clonally may have clinical significance in disease evolution and require further investigation.
ACTA NEUROPATHOLOGICA
(2022)
