Article
Gastroenterology & Hepatology
Ni Zhen, Jiabei Zhu, Siwei Mao, Qi Zhang, Song Gu, Ji Ma, Yue Zhang, Minzhi Yin, Haojie Li, Nan Huang, Han Wu, Fenyong Sun, Binwu Ying, Lin Zhou, Qiuhui Pan
Summary: This study reveals aberrant alternative splicing in hepatoblastoma (HB), including the intron retention of long non-coding RNAs from the SNHG family. Furthermore, the interaction between PABPN1 and the splicing machinery in HB is involved in promoting cell proliferation and DNA damage repair via inducing the intron retention of SNHG19. Knockdown of PABPN1 increases the cisplatin sensitivity of HB PDOs.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Agricultural Engineering
Bing He, Xin Han, Hailin Liu, Mengjia Bu, Peng Cui, Li-an Xu
Summary: This study revealed the genome-wide landscape of alternative splicing (AS) patterns in G. biloba, a relict tree species with rich medicinal value. Intron retention was found to be the dominant AS type, and the AS patterns of important secondary metabolites in G. biloba were analyzed. These findings have important implications for studying gene regulation and the synthesis mechanisms of secondary metabolites in woody plants.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Cell Biology
Despoina Kosmara, Sofia Papanikolaou, Christoforos Nikolaou, George Bertsias
Summary: Substantial evidence shows divergences in immune responses between men and women. Women are more susceptible to autoimmunity, while men suffer from more severe presentation of autoimmune disorders. This study revealed unprecedented variation in sex-dependent splicing events in systemic lupus erythematosus (SLE) patients and the healthy state, with potential implications for understanding the molecular basis of sexual dimorphism in autoimmunity.
Article
Plant Sciences
Dapu Liu, Zhikun Yu, Guoxia Zhang, Wenchao Yin, Lulu Li, Mei Niu, Wenjing Meng, Xiaoxing Zhang, Nana Dong, Jihong Liu, Yanzhao Yang, Shimei Wang, Chengcai Chu, Hongning Tong
Summary: By using CRSPR/Cas9 tools for genome editing, a panel of mutants within three BR signaling gene families were generated in rice, showing diverse plant phenotypes. The mutants exhibited functional redundancy, differentiation, or dominancy among the members within each family. These findings suggest that editing of BR-related family genes could be a feasible approach for screening desired plants in rice.
Article
Cell Biology
Meenakshi Sudhakaran, Tatiana Garcia Navarrete, Katherine Mejia-Guerra, Eric Mukundi, Timothy D. Eubank, Erich Grotewold, Daniel Arango, Andrea I. Doseff
Summary: Apigenin has been found to reprogram the transcriptome of triple-negative breast cancer (TNBC), inducing apoptosis and inhibiting tumor growth, offering new options for TNBC treatments.
CELL DEATH & DISEASE
(2023)
Article
Clinical Neurology
Hong-Dong Li, Cory C. Funk, Karen McFarland, Eric B. Dammer, Mariet Allen, Minerva M. Carrasquillo, Yona Levites, Paramita Chakrabarty, Jeremy D. Burgess, Xue Wang, Dennis Dickson, Nicholas T. Seyfried, Duc M. Duong, James J. Lah, Steven G. Younkin, Allan Levey, Gilbert S. Omenn, Nilufer Ertekin-Taner, Todd E. Golde, Nathan D. Price
Summary: In this study, intron retention (IR) was found to play a role in Alzheimer's disease (AD) through genome-wide analysis of genetic, transcriptomic, and proteomic data. Thousands of IR events were identified, along with differentially expressed genes associated with AD and splicing-related genes that may regulate IR. The findings provide a new resource for exploring new AD biomarkers and pathological mechanisms.
ALZHEIMERS & DEMENTIA
(2021)
Article
Genetics & Heredity
Zeru Li, Cheng Qin, Bangbo Zhao, Yuanyang Wang, Tianyu Li, Yutong Zhao, Weibin Wang
Summary: The study identified a new intron retention gene in pancreatic ductal adenocarcinoma, which is regulated by the upstream splicer DHX38. The reduction of DHX38 expression leads to the retention of the fourth intron of RELL2, causing nonsense-mediated mRNA decay and inhibiting apoptosis of pancreatic cancer cells, ultimately promoting drug resistance. This research provides a potential therapeutic target for pancreatic ductal adenocarcinoma.
Article
Biotechnology & Applied Microbiology
Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson, Abhinav Nellore
Summary: Short-read tools for detecting intron retention have poor performance and often result in false positives and false negatives, calling into question the completeness and validity of putatively retained introns called by commonly used methods.
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
Cell Biology
Deepak Kumar, Manoj K. Kashyap, Zhe Yu, Ide Spaanderman, Reymundo Villa, Thomas J. Kipps, James J. La Clair, Michael D. Burkart, Januario E. Castro
Summary: Alterations in RNA splicing are associated with malignancies. This study found that the RNA splicing modulators FD-895 and pladienolide B can induce higher apoptosis levels and inhibit solid tumor growth by modulating the Wnt signaling pathway and mRNA splicing.
Article
Biotechnology & Applied Microbiology
Fernando Diaz, Carson W. Allan, Therese Ann Markow, Jeremy M. Bono, Luciano M. Matzkin
Summary: Our study showed that genes with alternative splicing (AS) are significantly affected by heterospecific matings in female heads and evolve at slower rates than the genome background. However, genes with differential expression (DE) evolve at rates similar to, or even higher than, male reproductive genes, indicating their potential role in sexual selection and the evolution of reproductive barriers. Conspecific matings induced specific pathways related to amino acid balance, while heterospecific matings failed to regulate some of these genes and activated additional genes. Functional specializations were observed with DE genes related to proteolysis and nutrient homeostasis, while AS genes were associated with photoreception and muscle assembly pathways. Intron retention (IR) seems to play a more general role in DE regulation during the female postmating response.
Article
Biochemistry & Molecular Biology
Yasutaka Yamanaka, Takaki Ishizuka, Ken-ichi Fujita, Naoko Fujiwara, Masashi Kurata, Seiji Masuda
Summary: Calcium homeostasis endoplasmic reticulum protein (CHERP) is involved in the regulation of alternative splicing by interacting with U2 snRNPs and U2 snRNP-related proteins, leading to the accumulation of poly(A)(+) RNAs in the nucleus. CHERP depletion also induces anomalies in cell cycle progression and cell division.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Qiufang Guo, Ping Zhang, Wenjing Ying, Yaqiong Wang, Jitao Zhu, Gang Li, Huijun Wang, Xiaochuan Wang, Caixia Lei, Wenhao Zhou, Jinqiao Sun, Bingbing Wu
Summary: We reported a novel intronic mutation of DKC1 causing dyskerin functional loss in a Chinese family. This mutation may influence normal physiological function and is associated with still birth or early death. The finding expands the spectrum of pathogenic DKC1 gene mutations and can be used in molecular diagnosis.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2022)
Article
Multidisciplinary Sciences
Natalie M. Clark, Trevor M. Nolan, Ping Wang, Gaoyuan Song, Christian Montes, Conner T. Valentine, Hongqing Guo, Rosangela Sozzani, Yanhai Yin, Justin W. Walley
Summary: This study analyzed the BR signaling in Arabidopsis by integrating multiple omics datasets and inferring networks, identifying a BR-regulated transcription factor BRONTOSAURUS that affects cell division in roots. The research provides insights into the molecular signaling events during BR response through integrative network analysis applied to multi-omic data.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Soyun Kim, Hayoung Song, Yoonkang Hur
Summary: This study found that the overexpression of intron-retained forms of the RsMYB1 and RsTT8 genes in radish can significantly increase anthocyanin accumulation in plants. However, these retained intron forms encode proteins that cannot form the MBW complex, yet their co-expression in tobacco leaves leads to higher anthocyanin accumulation.
PLANT CELL REPORTS
(2021)
Article
Plant Sciences
Zhiyong Li, Yao Wang, Jian Huang, Nagib Ahsan, Gabriel Biener, Joel Paprocki, Jay J. Thelen, Valerica Raicu, Dazhong Zhao
Article
Multidisciplinary Sciences
Jian Huang, Zhiyong Li, Dazhong Zhao
Scientific Reports
(2016)
Article
Biochemistry & Molecular Biology
Jian Huang, Zhiyong Li, Gabriel Biener, Erhui Xiong, Shikha Malik, Nathan Eaton, Catherine Z. Zhao, Valerica Raicu, Hongzhi Kong, Dazhong Zhao
Article
Plant Sciences
Likai Wang, Huangwei Chu, Zhiyong Li, Juan Wang, Jintao Li, Yang Qiao, Yanru Fu, Tongmin Mou, Chunli Chen, Jian Xu
Article
Biochemistry & Molecular Biology
Zhiyong Li, Yi Chen, Dauenpen Meesapyodsuk, Xiao Qiu
Article
Biochemical Research Methods
Erhui Xiong, Zhiyong Li, Chen Zhang, Jing Zhang, Ye Liu, Ting Peng, Zhen Chen, Quanzhi Zhao
Summary: Leaf senescence is a complex, genetically regulated process in rice. By studying rice leaf-senescence genes, researchers can gain a better understanding of the molecular mechanisms underlying leaf senescence, ultimately leading to increased grain yields.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agronomy
Mao-Wei Guo, Lin Zhu, Hong-Yan Li, Zi-Nian Wu, Zhi-Yong Li, Jun Li
Summary: The study evaluated the expression stability of nine candidate reference genes under different experimental conditions, with EF-1alpha found to be a more stable reference gene in different subsets. It can be used simultaneously for normalizing mRNA and miRNA expression, facilitating genetic studies of this leguminous plant.
GENETIC RESOURCES AND CROP EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Zhiyong Li, Yajuan Fu, Jinyu Shen, Jiansheng Liang
Summary: WNK8 gene expression is post-transcriptionally regulated through an upstream open reading frame (uORF) in its 5' untranslated region, causing ribosome stalling. WNK8 and its downstream target RACK1 synergistically coordinate ABA signaling rather than antagonistically modulating glucose response and flowering.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Maowei Guo, Hongyan Li, Lin Zhu, Zinian Wu, Jun Li, Zhiyong Li
Summary: The study explored genes conferring drought resistance to Medicago ruthenica through analyzing miRNAs and their potential target genes under osmotic stress conditions. The study identified 591 miRNAs and predicted 11 target genes, showing that miR319-TCP4 module may act as a homeostasis factor in M. ruthenica roots following drought injury. This module is conserved among plant species.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Jinyu Shen, Zhiyong Li, Yajuan Fu, Jiansheng Liang
Summary: This study focused on the characterization of the spliced variants of beta CA1 from Arabidopsis, revealing different subcellular and tissue distributions and responses to environmental stimuli. Furthermore, the physiological role of beta CA1 in heat stress response and its protein-protein interaction network were also addressed, suggesting new avenues for future investigations.
Article
Biochemistry & Molecular Biology
Hui-Yuan Zhang, Ze-Hao Hou, Yan Zhang, Zhi-Yong Li, Jun Chen, Yong-Bin Zhou, Ming Chen, Jin-Dong Fu, You-Zhi Ma, Hui Zhang, Zhao-Shi Xu
Summary: The soybean GmEF8 gene plays a positive role in regulating drought and heat stresses in Arabidopsis and soybean, and its overexpression enhances the plants' tolerance to these stresses.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Plant Sciences
Lin Zhu, Hongyan Li, Zinian Wu, Zhiyong Li, Maowei Guo, Bu Ning, Wanpeng Liu, Qian Liu, Lei Liu, Zhiyong Wang, Jun Li, Fugui Mi
Summary: Medicago ruthenica, a wild legume forage, exhibits high genetic and phenotypic variation. A purely yellow flower variety (YFM) of M. ruthenica with distinct characteristics from the purple flower variety (PFM) has been discovered. This study investigated M. ruthenica using targeted metabolomics and transcriptomics, revealing differences in flavonoid content and gene expression related to flower coloration. The findings suggest that YFM is a variety of M. ruthenica rather than a different species, and provide insights for further research on species with similar morphologies.
Article
Biochemistry & Molecular Biology
Jan Masood, Wei Zhu, Yajuan Fu, Zhiyong Li, Yeling Zhou, Dong Zhang, Huihui Han, Yan Yan, Xing Wen, Hongwei Guo, Jiansheng Liang
Summary: Plants use versatile scaffold proteins to facilitate communication between different signaling pathways. This study shows that the scaffold protein RACK1A is involved in leaf senescence mediated by ethylene signaling, through the coordination of the EIN3-miR164-ORE1 transcriptional cascade. RACK1A acts as a positive regulator of ethylene-mediated leaf senescence by promoting EIN3 protein accumulation and enhancing its DNA-binding activity. This study provides insights into how scaffold proteins regulate phytohormone signaling to control plant development.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Plant Sciences
Zhiyong Li, Yajuan Fu, Yuzhu Wang, Jiansheng Liang
Summary: This study reveals that the scaffold protein RACK1 is involved in the BR signaling pathway in Arabidopsis by mediating the nuclear localization of BZR1. RACK1 interacts with BZR1 and competes with 14-3-3 proteins, leading to enhanced nuclear localization of BZR1. Furthermore, BR treatment disrupts the interaction between 14-3-3 and RACK1/BZR1, promoting the nuclear localization of BZR1.