Review
Plant Sciences
Xiao-Xiao Liu, Qian-Huan Guo, Wei-Bo Xu, Peng Liu, Kang Yan
Summary: Plants use diverse strategies and complex regulations to adapt to changing environmental conditions. In addition to direct gene transcription regulation, alternative splicing plays a crucial role in coping with various stresses.
FRONTIERS IN PLANT SCIENCE
(2022)
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)
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.
Article
Genetics & Heredity
Changsheng Shao, Fangfang Cai, Yanping Zhang, Zhiru Bao, Gehui Shi, Manzhu Bao, Jiaqi Zhang
Summary: This study provides insights into the regulatory mechanisms of alternative splicing (AS) in plants, showing that AS signals are distributed within the introns where the splice sites are present and may also be present in exons or other introns.
Article
Biotechnology & Applied Microbiology
Lin Wang, Karin Shamardani, Husam Babikir, Francisca Catalan, Takahide Nejo, Susan Chang, Joanna J. Phillips, Hideho Okada, Aaron A. Diaz
Summary: RNA sequencing analysis of 37 primary-recurrent paired human GBM specimens revealed the landscape of alternative splicing in recurrent GBM, identifying cell-type-specific splicing patterns and new targets, as well as recurrent-specific gene isoforms. These studies shed light on gene expression in recurrent GBM and identify novel targets for therapeutic development.
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
Florian Le Billan, Gloria Umogbai, Carolyn L. Cummins
Summary: Steroid hormones not only regulate gene transcription but also modulate the alternative splicing of pre-mRNA, acting through binding to nuclear receptors. The effect of steroid hormones on alternative splicing is time-, gene-, and tissue-specific. Mechanisms by which steroid hormones regulate alternative splicing include the recruitment of dual-function proteins, transcriptional regulation of splicing factor levels, alternative splicing of splicing factors or transcription factors, and regulation of elongation rate.
Review
Cell Biology
Galia Maik-Rachline, Inbal Wortzel, Rony Seger
Summary: The MAPK cascades transmit external stimuli signals to various cellular processes through specific phosphorylation and activation, ensuring proper cell fate. The involvement of specific genes and alternatively spliced isoforms extends the signaling specificity of the MAPK cascades, enabling different cellular responses to various stimuli.
Review
Plant Sciences
Sheeba John, Justyna Jadwiga Olas, Bernd Mueller-Roeber
Summary: Plants have evolved molecular strategies to cope with environmental temperature changes, including alternative splicing to enable favorable growth responses. Studying these splicing events is crucial for understanding how plants adapt to temperature fluctuations.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Plant Sciences
Remus R. E. Rosenkranz, Sarah Ullrich, Karin Loechli, Stefan Simm, Sotirios Fragkostefanakis
Summary: Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, and it is considered as an integral part of the heat stress response. However, our understanding of the regulation of heat stress-sensitive AS in plants is still limited.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Peng Gao, Teagen D. Quilichini, Chun Zhai, Li Qin, Kirby T. Nilsen, Qiang Li, Andrew G. Sharpe, Leon Kochian, Jitao Zou, Anireddy S. N. Reddy, Yangdou Wei, Curtis Pozniak, Nii Patterson, C. Stewart Gillmor, Raju Datla, Daoquan Xiang
Summary: Research indicates that there is diversity in the regulation of alternative splicing in polyploid wheat and grass species, not only showing differences in different tissues but also between subgenomes. Analysis of homoeologous triads in polyploid wheat reveals evolutionary divergence in the regulation of embryogenesis between gene-level and transcript-level.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
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)
Article
Plant Sciences
Hong Yang, Ping Li, Guihua Jin, Daping Gui, Li Liu, Chengjun Zhang
Summary: Plant adaptation to drought stress is crucial for survival and crop yield. This study investigated the genetic mechanism underlying drought memory by analyzing alternative splicing events in response to drought stress in rice. Exon skipping was identified as the predominant type of alternative splicing, with variable frequencies observed in different plant species. The study also suggested that drought stress may increase U12-type splicing, leading to an increase in exon skipping frequency. Furthermore, potential transcription factors and hub genes related to drought memory were identified.
Editorial Material
Biochemistry & Molecular Biology
Pooja Singh, Ehsan Pashay Ahi
Summary: Alternative splicing is a widely present co-transcriptional gene regulatory mechanism in plants, animals and fungi, contributing to transcriptomic and proteomic diversity. Recent research suggests that alternative splicing plays a crucial role in ecological adaptations, highlighting its importance in adaptive evolution and speciation.
Article
Multidisciplinary Sciences
Runxian Yu, Chenyu Sun, Ying Liu, Renchao Zhou
Summary: Shifts from cis-to trans-splicing of mitochondrial introns may not be uncommon among angiosperms, as evidenced by the study on Tolypanthus maclurei, a hemiparasitic plant from the family Loranthaceae (Santalales). In addition to five shared trans-spliced introns in seed plants, this species exhibited shifts in splicing patterns for additional introns, including two specific to T. maclurei. Furthermore, a chimeric gene atp1 in its mitogenome suggested horizontal gene transfer from Lamiales.
Article
Hematology
Shunsuke Kimura, Lindsey Montefiori, Ilaria Iacobucci, Yaqi Zhao, Qingsong Gao, Elisabeth M. Paietta, Claudia Haferlach, A. Douglas Laird, Paul E. Mead, Zhaohui Gu, Wendy Stock, Mark Litzow, Jacob M. Rowe, Selina M. Luger, Stephen P. Hunger, Georgina L. Ryland, Breon Schmidt, Paul G. Ekert, Alicia Oshlack, Sean M. Grimmond, Jacqueline Rehn, James Breen, David Yeung, Deborah L. White, Ibrahim Aldoss, Elias J. Jabbour, Ching-Hon Pui, Manja Meggendorfer, Wencke Walter, Wolfgang Kern, Torsten Haferlach, Samuel Brady, Jinghui Zhang, Kathryn G. Roberts, Piers Blombery, Charles G. Mullighan
Summary: This study identified a previously unrecognized high-risk subtype of B-ALL using transcriptome and whole-genome sequencing. The subtype is characterized by specific gene expression profile and genomic alterations caused by abnormal activation of recombination-activating genes (RAG). It is associated with high-risk clinical features.
Article
Oncology
Bappaditya Chandra, Nicole L. Michmerhuizen, Hazheen K. Shirnekhi, Swarnendu Tripathi, Brittany J. Pioso, David W. Baggett, Diana M. Mitrea, Ilaria Iacobucci, Michael R. White, Jingjing Chen, Cheon-Gil Park, Huiyun Wu, Stanley Pounds, Anna Medyukhina, Khaled Khairy, Qingsong Gao, Chunxu Qu, Sherif Abdelhamed, Scott D. Gorman, Simranjot Bawa, Carolyn Maslanka, Swati Kinger, Priyanka Dogra, Mylene C. Ferrolino, Danika Di Giacomo, Cristina Mecucci, Jeffery M. Klco, Charles G. Mullighan, Richard W. Kriwacki
Article
Biology
Xudong Zou, Bernhard Schaefke, Yisheng Li, Fujian Jia, Wei Sun, Guipeng Li, Weizheng Liang, Tristan Reif, Florian Heyd, Qingsong Gao, Shuye Tian, Yanping Li, Yisen Tang, Liang Fang, Yuhui Hu, Wei Chen
Summary: Research has found that alternative splicing is widespread in mammalian tissues and may be related to tissue-dependent regulation. Micro-exons have high inclusion levels in the brain. Splicing divergence appears to be mainly non-adaptive and may be related to trans-regulatory splicing efficiency.
LIFE SCIENCE ALLIANCE
(2022)
Article
Immunology
Mohammad Arabpour, Cristina Lebrero-Fernandez, Karin Schon, Anneli Stromberg, Vanja Borjesson, Katharina Lahl, Marlies Ballegeer, Xavier Saelens, Davide Angeletti, William Agace, Nils Lycke
Summary: Migratory dendritic cells expressing CD103 are important targets for mucosal vaccines. These cells can be divided into two subsets, cDC1 and cDC2, which are responsible for activating functionally distinct CD4 T cells. Recent studies have shown that cDC2 cells have overlapping functions with cDC1 cells, but the plasticity of cDC1 cells has not been reported. A genetically engineered vaccine adjuvant platform targeting CD103(+) cDC1 and cDC2 cells was developed, and it was found that this adjuvant modified cDC1 cells to effectively prime Th17 cells, a function previously limited to cDC2 cells. Further analysis revealed that cDC2 cells were dispensable, while cDC1 cells were critical for immune responses.
MUCOSAL IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Jasmin Bartl, Marco Zanini, Flavia Bernardi, Antoine Forget, Lena Bluemel, Julie Talbot, Daniel Picard, Nan Qin, Gabriele Cancila, Qingsong Gao, Soumav Nath, Idriss Mahoungou Koumba, Marietta Wolter, Francois Kuonen, Maike Langini, Thomas Beez, Christopher Munoz, David Pauck, Viktoria Marquardt, Hua Yu, Judith Souphron, Mascha Korsch, Christina Moelders, Daniel Berger, Sarah Goebbels, Frauke-Dorothee Meyer, Bjorn Scheffler, Barak Rotblat, Sven Diederichs, Vijay Ramaswamy, Hiromishi Suzuki, Anthony Oro, Kai Stuehler, Anja Stefanski, Ute Fischer, Gabriel Leprivier, Dieter Willbold, Gerhard Steger, Alexander Buell, Marcel Kool, Peter Lichter, Stefan M. Pfister, Paul A. Northcott, Michael D. Taylor, Arndt Borkhardt, Guido Reifenberger, Olivier Ayrault, Marc Remke
Summary: Long non-coding RNA (lncRNA) HHIP-AS1 stabilizes the mRNA of dynein complex 1, thereby promoting the pro-mitotic effects of SHH-driven tumors.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Bingchen Yu, Shanshan Li, Takako Tabata, Nanxi Wang, Li Cao, G. Renuka Kumar, Wei Sun, Jun Liu, Melanie Ott, Lei Wang
Summary: This study developed covalent nanobodies that bind irreversibly with SARS-CoV-2, increasing neutralization potency against wild-type virus and its variants. These insights into increased potency can be valuable for developing effective therapeutics against viral infections.
Article
Multidisciplinary Sciences
Kyle S. Smith, Laure Bihannic, Brian L. Gudenas, Parthiv Haldipur, Ran Tao, Qingsong Gao, Yiran Li, Kimberly A. Aldinger, Igor Y. Iskusnykh, Victor V. Chizhikov, Matthew Scoggins, Silu Zhang, Angela Edwards, Mei Deng, Ian A. Glass, Lynne M. Overman, Jake Millman, Alexandria H. Sjoboen, Jennifer Hadley, Joseph Golser, Kshitij Mankad, Heather Sheppard, Arzu Onar-Thomas, Amar Gajjar, Giles W. Robinson, Volker Hovestadt, Brent A. Orr, Zoltan Patay, Kathleen J. Millen, Paul A. Northcott
Summary: Medulloblastoma, a malignant childhood cerebellar tumour, has different subgroups with distinct developmental origins. Multi-omics analysis connects the molecular features of medulloblastoma subgroups to their origins during early development.
Article
Chemistry, Multidisciplinary
Shanshan Li, Nanxi Wang, Bingchen Yu, Wei Sun, Lei Wang
Summary: Protein-carbohydrate interactions are important in biological processes but challenging to study. This study engineered covalent linkages between proteins and carbohydrates, offering a solution to overcome the low affinity and weak strength of these interactions.
Article
Chemistry, Multidisciplinary
Wei Sun, Nanxi Wang, Hongjiang Liu, Bingchen Yu, Ling Jin, Xingjie Ren, Yin Shen, Lei Wang
Summary: Protein-RNA interactions play a crucial role in regulating the fate and function of RNA. This study demonstrates a novel approach, using genetically encoded unnatural amino acids, to crosslink proteins with bound RNA and analyze their interactions. The technique allows for the identification of specific RNA molecules and the discovery of unknown chemical modifications in cells. This research is highly significant in advancing our understanding of protein-RNA interactions in biological processes.
Meeting Abstract
Hematology
Heiko Mueller, Wencke Walter, Stephan Hutter, Niroshan Nadarajah, Frank Dicker, Manja Meggendorfer, Qingsong Gao, Ilaria Iacobucci, Charles G. Mullighan, Wolfgang Kern, Torsten Haferlach, Claudia Haferlach
Article
Psychology, Multidisciplinary
Qingsong Gao, Yongxia Wei
Summary: Nowadays, colleges and universities are paying increasing attention to the mental health of college students and have conducted a wide range of mental health promotion activities. This study proposes a deep learning algorithm based on convolutional neural networks to integrate deep learning with classroom teaching. The research aims to explore the development and application of a cultivation mechanism for mental health education of college students in campus culture creation from the perspective of deep learning. The study aims to understand college students' mental health training in campus culture creation and develop experimental outcomes of mental health education courses for college students. Finally, investigations, statistics, and analysis related to college students' mental health are carried out in the current situation in China. The experimental results show that 62 out of 156 schools provide both mandatory and optional mental health education courses for college students. According to a student questionnaire survey, 86.7% of respondents believe it is crucial to establish mental health-related educational courses, and 61.9% believe that compulsory courses should be established, with students wanting to add group guidance or activities to enhance their experience and participation.
CURRENT PSYCHOLOGY
(2023)
Meeting Abstract
Oncology
Nicole Michmerhuizen, Bappaditya Chandra, Hazheen Shirnekhi, Swarnendu Tripathi, Brittany Pioso, David Baggett, Diana Mitrea, Ilaria Iacobucci, Michael White, Jingjing Chen, Cheon-Gil Park, Huiyun Wu, Stanley Pounds, Anna Medyukhina, Khaled Khairy, Qingsong Gao, Chunxu Qu, Scott Gorman, Simran Bawa, Carolyn Maslanka, Swati Kinger, Priyanka Dogra, Danika Di Giacomo, Cristina Mecucci, Jeffery Klco, Charles Mullighan, Richard Kriwacki
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2022)
Meeting Abstract
Oncology
Kyle Smith, Laure Bihannic, Brian Gudenas, Qingsong Gao, Parthiv Haldipur, Ran Tao, Igor Iskusnykh, Viktor Chizhikov, Matthew Scoggins, Silu Zhang, Angela Edwards, Mei Deng, Ian Glass, Lynne Overman, Jake Millman, Alexandria Sjoboen, Jennifer Hadley, Kshitij Mankad, Arzu Onar-Thomas, Amar Gajjar, Giles Robinson, Kimberly Aldinger, Volker Hovestadt, Heather Tillman, Brent Orr, Zoltan Patay, Kathleen Millen, Paul Northcott
Article
Oncology
Kirsten M. Dickerson, Chunxu Qu, Qingsong Gao, Ilaria Iacobucci, Zhaohui Gu, Hiroki Yoshihara, Emily A. Backhaus, Yunchao Chang, Laura J. Janke, Beisi Xu, Gang Wu, Evangelia K. Papachristou, Clive S. D'Santos, Kathryn G. Roberts, Charles G. Mullighan
Summary: ZNF384-rearranged fusion oncoproteins play a crucial role in hematopoiesis and leukemia development by promoting hematopoietic cell expansion and skewing the differentiation direction. The expression of ZNF384 FO can disrupt specific genes in hematopoietic stem cells, potentially leading to leukemia.
BLOOD CANCER DISCOVERY
(2022)