Article
Genetics & Heredity
Haiyang Dong, Lei Li, Xiaohua Zhu, Jilong Shi, Ying Fu, Shixin Zhang, Yang Shi, Bingbing Xu, Jian Zhang, Feng Shi, Yongfeng Jin
Summary: Our study identified evidence of evolutionarily conserved RNA base pairings mediating mutually exclusive splicing in the exon 4 cluster of Dscam1 in Coleoptera species. In contrast to fly species, most exon 6 selector sequences are partially located in the variable exon region in Coleoptera species. Additionally, bidirectional RNA-RNA interactions were predicted to regulate mutually exclusive splicing of variable exon 9 of Dscam1.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Xue-Ling Mao, Zi-Han Li, Meng-Han Huang, Jin-Tao Wang, Jing-Bo Zhou, Qing-Run Li, Hong Xu, Xi-Jin Wang, Xiao-Long Zhou
Summary: This study revealed the presence of METTL2A and METTL2B in vivo, and successfully demonstrated their m(3)C32 modification activity on tRNA(Thr) and tRNA(ser)(GCU) in vitro. The research also found that G35 and t(6)A37 are essential for tRNA(Thr) m(3)C32 formation, while the anticodon loop and long arm are crucial for tRNA(ser)(GCU) m(3)C32 biogenesis.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Natalia Bartys, Anna Pasternak, Jolanta Lisowiec-Wachnicka
Summary: This article presents detailed research on the optimization of bifunctional antisense oligonucleotides (BASOs) for modulating alternative splicing. The authors demonstrate the effectiveness of BASOs in regulating mutually exclusive alternative splicing of the PKM gene.
Article
Plant Sciences
Yanwei Wang, Zhimin Yang, Meng Zhang, Pengfei Ai
Summary: This study identified the crucial role of the rice SSA1 gene in chloroplast biogenesis. SSA1 regulates early chloroplast development and is involved in RNA editing and intron splicing. These findings contribute to the understanding of molecular mechanisms underlying chloroplast generation.
Article
Fisheries
Xiao-Li Zhang, Guo-Qing Shen, Xiao-Na Zhang, Yue-Hong Zhao, Wei-Wei Li, Qun Wang
Summary: In arthropods, Dscam gene exists as numerous splice variants, and we discovered additional splice variants for exons 6 and 14 in Chinese mitten crab. There may be more than 50,000 Dscam protein variants in E. sinensis. EsDscam-Ig1-Ig7 was found to bind to bacteria and promote hemocyte phagocytosis and bacterial removal, providing immune defense against bacterial infection.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Biology
Minato Hirano, Gaddiel Galarza-Munoz, Chloe Nagasawa, Geraldine Schott, Liuyang Wang, Alejandro L. Antonia, Vaibhav Jain, Xiaoying Yu, Steven G. Widen, Farren B. S. Briggs, Simon G. Gregory, Dennis C. Ko, William S. Fagg, Shelton Bradrick, Mariano A. Garcia-Blanco
Summary: This study identified genes associated with increased susceptibility to multiple sclerosis (MS) and revealed the important role of DDX39B gene in immune tolerance by controlling the expression of MS susceptibility genes and immune-related genes.
Article
Biochemistry & Molecular Biology
Hang Yang, Yunlong Wang, Yunlu Tian, Xuan Teng, Zehui Lv, Jie Lei, Erchao Duan, Hui Dong, Xue Yang, Yuanyan Zhang, Yinglun Sun, Xiaoli Chen, Xiuhao Bao, Rongbo Chen, Chuanwei Gu, Yipeng Zhang, Xiaokang Jiang, Wenyu Ma, Pengcheng Zhang, Yi Ji, Yu Zhang, Yihua Wang, Jianmin Wan
Summary: A mutant rice flo22 showed delayed amyloplast development in endosperm cells, affecting mitochondrial morphology and function. Flo22, encoding a mitochondrion-localized P-type PPR protein, mutations led to defective trans-splicing of mitochondrial nad1 intron 1 and affected complex I assembly and activity. Additionally, FLO22 interacted with DYW3 and participated in mitochondrial RNA editing.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Virology
Wei Zou, Gau Shoua Vue, Benedetta Assetta, Heather Manza, Walter J. Atwood, Michael J. Imperiale
Summary: BK polyomavirus is a common human pathogen that can cause complications in the kidneys and bladder. The viral intron may be spliced out from primary RNA transcripts that circulate multiple times, providing a mechanism for expressing viral miRNA.
JOURNAL OF VIROLOGY
(2021)
Article
Biology
Huanping Guo, Lin Xia, Wei Wang, Wei Xu, Xipeng Shen, Xiao Wu, Tong He, Xuelin Jiang, Yinying Xu, Pan Zhao, Dongmei Tan, Xi Zhang, Yunfang Zhang
Summary: This study explores the tissue-specific distribution pattern of RNA modifications in mouse tissues under hypobaric hypoxia exposure. The abundance of RNA modifications is found to be tissue-specific and responsive to hypoxia exposure. Dysregulation of tRNA modifications under hypoxia attenuates cell proliferation rate and affects overall protein synthesis.
Article
Plant Sciences
Jie Qian, Meng Li, Min Zheng, Yi-Feng Hsu
Summary: The study revealed the important role of Arabidopsis SSB1 in ABA signaling and mitochondrial RNA splicing, associated with ABA sensitivity and salt stress response.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Social Issues
Buhari Dogan, Sudeshna Ghosh, Dung Phuong Hoang, Lan Khanh Chu
Summary: The objective of this study is to examine the major drivers of energy consumption and carbon dioxide emissions in the context of G7 and E7 countries. It found that eco-innovation is effective in reducing energy use intensity and controlling carbon emissions in G7 countries, but harmful in E7 countries. The study also identified an inverted U-shaped relationship between economic complexity and carbon emissions in G7 countries, while E7 countries experience a U-shaped relationship. Institutions and globalization were found to be significant determinants of environmental quality in both sets of countries. The study highlights the importance of reinforcing eco-technology application in G7 countries and optimizing gains from globalization in E7 countries for energy efficiency and carbon abatement strategies.
TECHNOLOGY IN SOCIETY
(2022)
Article
Plant Sciences
Hee Tae Lee, Hyo-Young Park, Keh Chien Lee, Jeong Hwan Lee, Jeong-Kook Kim
Summary: We investigated the transcriptomic changes in shoot apices during floral transition in Arabidopsis mutants of splicing factors AtU2AF65a and AtU2AF65b. AtU2AF65a mutants showed delayed flowering, while AtU2AF65b mutants exhibited accelerated flowering. RNA-seq analysis revealed that AtU2AF65a mutants had more differentially expressed genes compared to AtU2AF65b mutants. The gene FLOWERING LOCUS C (FLC), a major floral repressor, was significantly up- or down-regulated in the mutants. Additionally, the expression and alternative splicing patterns of several FLC upstream regulators were altered in the mutants. Our findings suggest that AtU2AF65a and AtU2AF65b splicing factors modulate FLC expression by affecting the expression or AS patterns of FLC upstream regulators, leading to different flowering phenotypes.
Article
Cell Biology
Yusuke Yagi, Takamasa Teramoto, Shuji Kaieda, Takayoshi Imai, Tadamasa Sasaki, Maiko Yagi, Nana Maekawa, Takahiro Nakamura
Summary: This article introduces a protein-based RNA manipulation technology using proteins containing PPR motifs. By developing a rapid construction and evaluation method, researchers successfully constructed dozens of functional designer PPR proteins that can target specific 18 nt-long RNA molecules and control cellular functionality.
Article
Oncology
Alimu Wufuer, Xiemusiye Luohemanjiang, Lei Du, Jing Lei, Mayila Shabier, Deng Feng Han, Jianhua Ma
Summary: This study assessed the potential function of antisense non-coding RNA in the INK4 locus (ANRIL) in gene expression and alternative splicing. The results showed that ANRIL overexpression affects the transcription levels of genes associated with the inflammatory response, NF-kappa B signaling pathway, type I interferon-mediated signal transduction pathway, and innate immune response. ANRIL also regulates the alternative splicing of hundreds of genes, many of which play key roles in the inflammatory response. By regulating alternative splicing and transcription, ANRIL is involved in regulating the inflammatory response mechanisms.
MOLECULAR MEDICINE REPORTS
(2023)
Article
Oncology
Esmee Koedoot, Eline van Steijn, Marjolein Vermeer, Roman Gonzalez-Prieto, Alfred C. O. Vertegaal, John W. M. Martens, Sylvia E. Le Devedec, Bob van de Water
Summary: This study systematically evaluated the role of RNA splicing factors in TNBC cell proliferation by targeting 244 individual splicing factors. Nine splicing factors were identified as controlling proliferation of breast cancer cells through effective sororin splicing and appropriate sister chromatid cohesion, indicating potential targets for TNBC treatment. The identification of SUN2 as a critical component in the spliceosome complex interacting with sororin provides new insights into the mechanisms of TNBC proliferation.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2021)
Editorial Material
Gastroenterology & Hepatology
Wei Zhuo, Yiman Liu, Shuang Li, Dongyang Guo, Qiang Sun, Juan Jin, Xianping Rao, Mengjie Li, Meng Sun, Mingchun Jiang, Yanjun Xu, Lisong Teng, Yongfeng Jin, Jianmin Si, Wei Liu, Yibin Kang, Tianhua Zhou
Article
Biochemistry & Molecular Biology
Bingbing Xu, Yang Shi, Yandan Wu, Yijun Meng, Yongfeng Jin
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2019)
Article
Biochemistry & Molecular Biology
Weiling Hong, Yang Shi, Bingbing Xu, Yongfeng Jin
Article
Multidisciplinary Sciences
Fengyan Zhou, Guozheng Cao, Songjun Dai, Guo Li, Hao Li, Zhu Ding, Shouqing Hou, Bingbing Xu, Wendong You, Gil Wiseglass, Feng Shi, Xiaofeng Yang, Rotem Rubinstein, Yongfeng Jin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Review
Cell Biology
Bingbing Xu, Yijun Meng, Yongfeng Jin
Summary: Alternative splicing greatly expands transcriptomic and proteomic diversities in higher eukaryotes, with the splicing of long noncoding RNAs and back-/trans- splicing further enhancing the regulatory repertoire. RNA structures play a crucial role in regulating alternative splicing and back-splicing processes, and novel sequencing technologies have allowed for the identification of genome-wide RNA structures and interaction networks, providing new insights into RNA splicing regulation. The emerging transcription-folding-splicing paradigm is revolutionizing our understanding of RNA alternative splicing regulation and its impact on human diseases.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Genetics & Heredity
Haiyang Dong, Lei Li, Xiaohua Zhu, Jilong Shi, Ying Fu, Shixin Zhang, Yang Shi, Bingbing Xu, Jian Zhang, Feng Shi, Yongfeng Jin
Summary: Our study identified evidence of evolutionarily conserved RNA base pairings mediating mutually exclusive splicing in the exon 4 cluster of Dscam1 in Coleoptera species. In contrast to fly species, most exon 6 selector sequences are partially located in the variable exon region in Coleoptera species. Additionally, bidirectional RNA-RNA interactions were predicted to regulate mutually exclusive splicing of variable exon 9 of Dscam1.
FRONTIERS IN GENETICS
(2021)
Article
Cell Biology
Weiling Hong, Jian Zhang, Haiyang Dong, Yang Shi, Hongru Ma, Fengyan Zhou, Bingbing Xu, Ying Fu, Shixin Zhang, Shouqing Hou, Guo Li, Yandan Wu, Shuo Chen, Xiaohua Zhu, Wendong You, Feng Shi, Xiaofeng Yang, Zhefeng Gong, Jianhua Huang, Yongfeng Jin
Summary: The study provides evidence that splicing bias of Drosophila Dscam1 is crucial for the axonal wiring of mushroom bodies, with different bias types influencing development and non-repulsive signaling of MB.
Article
Multidisciplinary Sciences
Haiyang Dong, Bingbing Xu, Pengjuan Guo, Jian Zhang, Xi Yang, Lei Li, Ying Fu, Jilong Shi, Shixin Zhang, Yanda Zhu, Yang Shi, Fengyan Zhou, Lina Bian, Wendong You, Feng Shi, Xiaofeng Yang, Jianhua Huang, Haihuai He, Yongfeng Jin
Summary: Researchers have discovered a set of hidden RNA secondary structures that balance the stochastic choice of splice variants in fruit flies. These structures enhance the inclusion of certain exons by forming a stronger pre-mRNA structure, while simultaneously repressing the inclusion of other exons by antagonizing their docking site-selector pairings.
Article
Biochemistry & Molecular Biology
Jinrui Zhang, Ge Zhang, Wenjing Zhang, Lu Bai, Luning Wang, Tiantian Li, Li Yan, Yang Xu, Dan Chen, Wenting Gao, Chuanzhou Gao, Chaoqun Chen, Menglin Ren, Yuexia Jiao, Hongqiang Qin, Yu Sun, Lili Zhi, Yangfan Qi, Jinyao Zhao, Quentin Liu, Han Liu, Yang Wang
Summary: The RNA binding protein RBMS1 is prevalent in immune-cold triple-negative breast cancers (TNBC) and plays a role in regulating the stability of programmed death ligand 1 (PD-L1). Depletion of RBMS1 enhances cytotoxic T cell mediated anti-tumor immunity and combination with immune checkpoint blockade or CAR-T treatment further enhances anti-tumor T-cell immunity. Our findings provide a new immunotherapeutic strategy targeting the immunosuppressive RBMS1 in TNBC.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Biochemistry & Molecular Biology
Haiyang Dong, Pengjuan Guo, Jian Zhang, Lili Wu, Ying Fu, Lei Li, Yanda Zhu, Yiwen Du, Jilong Shi, Shixin Zhang, Guo Li, Bingbing Xu, Lina Bian, Xiaohua Zhu, Wendong You, Feng Shi, Xiaofeng Yang, Jianhua Huang, Yongfeng Jin
Summary: Alternative splicing of Drosophila Dscam1 into a large number of isoforms provides a unique molecular code for neuronal self-recognition and self-avoidance. However, expressing only a single isoform leads to abnormal growth and segregation defects in axonal branches, suggesting a functional link between Dscam1 expression levels and isoform diversity.
Review
Biology
Bingbing Xu, Yanda Zhu, Changchang Cao, Hao Chen, Qiongli Jin, Guangnan Li, Junfeng Ma, Siwy Ling Yang, Jieyu Zhao, Jianghui Zhu, Yiliang Ding, Xianyang Fang, Yongfeng Jin, Chun Kit Kwok, Aiming Ren, Yue Wan, Zhiye Wang, Yuanchao Xue, Huakun Zhang, Qiangfeng Cliff Zhang, Yu Zhou
Summary: RNA structures play a crucial role in supporting RNA functions and regulation in various biological processes. This review highlights the importance of RNA structural studies and the development of novel technologies to decode genome-wide RNA structures and explore their functionalities across different species. The review also emphasizes the application of these new technologies in studying the structure landscape of the SARS-CoV-2 RNA genome. Furthermore, the review summarizes the diverse functions of RNA structures in different regulatory layers and physiological and pathological processes, and discusses future prospects for higher resolution mapping of the RNA structurome and deciphering novel modes of RNA structures and functions.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Shouqing Hou, Guo Li, Bingbing Xu, Haiyang Dong, Shixin Zhang, Ying Fu, Jilong Shi, Lei Li, Jiayan Fu, Feng Shi, Yijun Meng, Yongfeng Jin
Summary: The Down syndrome cell adhesion molecule 1 (Dscam1) gene generates tens of thousands of isoforms through alternative splicing, and trans-splicing markedly increases the repertoire of shortened Dscam (sDscam) isoforms in Tetranychus urticae. These trans-spliced sDscam isoforms exhibit cell adhesion ability and share the same binding specificity as their cis-spliced counterparts, providing molecular diversity and implications for neuronal and/or immune specificity.
Article
Medicine, Research & Experimental
Wenjing Zhang, Yu Sun, Lu Bai, Lili Zhi, Yun Yang, Qingzhi Zhao, Chaoqun Chen, Yangfan Qi, Wenting Gao, Wenxia He, Luning Wang, Dan Chen, Shujun Fan, Huan Chen, Hai-Long Piao, Qinglong Qiao, Zhaochao Xu, Jinrui Zhang, Jinyao Zhao, Sirui Zhang, Yue Yin, Chao Peng, Xiaoling Li, Quentin Liu, Han Liu, Yang Wang
Summary: RBMS1 is a key regulator of ferroptosis in lung cancer development and its high expression is associated with reduced patient survival. Depletion or inhibition of RBMS1 can promote ferroptosis and sensitize radioresistant lung cancer cells to radiotherapy. RBMS1 interacts with eIF3d to regulate translation of SLC7A11, playing a critical role in ferroptosis evasion during lung cancer progression.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Medicine, Research & Experimental
Yangfan Qi, Wei Han, Dan Chen, Jinyao Zhao, Lu Bai, Fang Huang, Zhenwei Dai, Gang Li, Chaoqun Chen, Wenjing Zhang, Jinrui Zhang, Bilian Jin, Yang Wang
Summary: Researchers developed Engineering circRNA regulators (ECRRs) to enhance circRNA biogenesis by combining RNA binding motifs of human Pumilio 1 with dimerization functional domains. The application of ECRRs could stimulate circRNA production of exogenous mini-gene reporters in a time- and dose-dependent manner with designed specificity. Moreover, ECRRs could promote the generation of endogenous circRNAs circ10720 and circBIRC6, offering a novel avenue to investigate circRNA biogenesis and manipulate disease-related circRNA production.
Article
Biochemistry & Molecular Biology
Yuesheng Lv, Wenjing Zhang, Jinyao Zhao, Bing Sun, Yangfan Qi, Haoyu Ji, Chaoqun Chen, Jinrui Zhang, Junxiu Sheng, Taishu Wang, Daniel Dominguez, Han Liu, Quentin Liu, Songshu Meng, Xiaoling Li, Yang Wang
Summary: SRSF1 is identified as an autophagy suppressor that inhibits autophagosome formation by promoting the splicing of Bcl-x and disrupting the Beclin1-PIK3C3 complex. The decrease of SRSF1 stabilizes the Beclin1 and PIK3C3 complex, activating autophagy, while starvation- and oxidative stresses-induced autophagy can degrade SRSF1 through interacting with LC3-II. This positive feedback mechanism is crucial for inhibiting Gefitinib-resistant cancer cell progression.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2021)
