Article
Biology
Xing Lin, Fei Liu, Kaifeng Meng, Hairong Liu, Yuanli Zhao, Yuanyuan Chen, Wei Hu, Daji Luo
Summary: Alternative splicing plays an important role in regulating gene functions in eukaryotes. Through global splicing analysis on zebrafish testes and ovaries, this study identified 120 differentially spliced genes and validated some of them. Functional enrichment analysis showed that these genes are involved in mRNA processing, mRNA metabolism, and microtubule-based processes. Interestingly, a high proportion of non-frameshift exon-skipping events were identified, indicating the potential functional significance of the alternative protein isoforms.
Article
Biochemistry & Molecular Biology
Naima Ahmed Fahmi, Heba Nassereddeen, Jaewoong Chang, Meeyeon Park, Hsinsung Yeh, Jiao Sun, Deliang Fan, Jeongsik Yong, Wei Zhang
Summary: AS-Quant is a robust program for identifying alternative splicing events from RNA-seq data. It outperforms other widely used tools by calculating read coverage, categorizing event types, and generating short read coverage plots. The significant alternative splicing events identified by AS-Quant were validated using RT-PCR experiments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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)
Article
Biochemistry & Molecular Biology
Yong Wang, Jialei Ji, Long Tong, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Honghao Lv
Summary: This study utilized SMRT sequencing to survey the full-length transcriptomes of five cabbage tissue types, discovering a large number of isoforms and conducting comprehensive analysis on alternative splicing (AS) and alternative polyadenylation (APA). It also revealed the presence of a significant number of genes related to resistance, as well as the identification of long non-coding RNAs (lncRNAs) and transcription factors (TFs).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Pharmacology & Pharmacy
Xiujing He, Jing Yu, Hubing Shi
Summary: This study investigated the relationship between alternative splicing characteristics and immune-related adverse events caused by immune checkpoint inhibitors through data mining, revealing potential predictive factors and shedding light on new mechanisms underlying irAEs.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Cell Biology
Sandhya Yadav, Deepak Pant, Atul Samaiya, Neetu Kalra, Sanjay Gupta, Sanjeev Shukla
Summary: Aberrant alternative splicing, particularly the upregulation of SRSF10, has been found to promote tumorigenesis in head and neck cancer patients by affecting key gene splice variants. The regulatory pathway involving EGR1 and the ERK1/2 pathway plays a crucial role in mediating the expression of SRSF10, highlighting the potential therapeutic target for better management of HNC patients.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yan Zheng, Landi Luo, Qian Chen, Danni Yang, Yuqiang Gong, Ya Yang, Xiangshi Qin, Yuhua Wang, Xiangxiang Kong, Yongping Yang
Summary: In this study, the cold response of D. catenatum was analyzed using RNA-Seq. The differentially expressed genes and differential alternative events related to cold stress were identified. Furthermore, the involvement of DcCBP20 in regulating alternative splicing and gene expression of cold-induced genes was discovered. This study contributes to our understanding of the role of AS genes in the cold stress response in D. catenatum.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Lili Dong, Jianan Wang, Guohua Wang
Summary: This article proposes a statistical framework and algorithm ASAS-EGB for ASAS analysis using the gene transcriptome. The framework can provide better inferential performance than using event isoforms and supports both single-end and paired-end RNA-seq data.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Genetics & Heredity
Guozhi Li, Dengxian Xu, Gang Huang, Quan Bi, Mao Yang, Haitao Shen, Hailiang Liu
Summary: This study revealed the important role of alternative splicing (AS) in regulating the drought response in Glycyrrhiza uralensis, particularly in nitrogen and protein metabolism. The mechanisms involve the spliceosomal pathway and basal transcription factor pathway.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Gaoyang Wang, Zuozhong Xie, Juan Su, Meishan Chen, Yanhua Du, Qian Gao, Guanxiong Zhang, Hailun Zhang, Xiang Chen, Hong Liu, Leng Han, Youqiong Ye
Summary: This study provides an in-depth analysis of immune-related alternative polyadenylation in cancer, identifying alternative polyadenylation events that may play a role in immune modulation and immunotherapy efficacy.
Article
Oncology
Xi-Tai Huang, Jian-Hui Li, Xiao-Xu Zhu, Chen-Song Huang, Zhuo-Xing Gao, Qiong-Cong Xu, Wei Zhao, Xiao-Yu Yin
Summary: HNRNPC regulates alternative splicing events to promote PDAC metastasis, with high expression correlating with poor prognosis. Knockdown of HNRNPC reduces PDAC cell invasion and metastasis, while overexpression enhances malignant phenotypes of PDAC cells.
Article
Biochemistry & Molecular Biology
Jing Liu, Shengcai Chen, Min Liu, Yimian Chen, Wei Fan, Seunghee Lee, Han Xiao, Dave Kudrna, Zixin Li, Xu Chen, Yaqi Peng, Kewei Tian, Bao Zhang, Rod A. Wing, Jianwei Zhang, Xuelu Wang
Summary: Alternative splicing plays a vital role in regulating nodule development in soybean during the interaction with Rhizobium, and our study provides comprehensive transcriptomic data on isoforms and long non-coding RNAs, contributing to future research in multiple directions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Jia Liu, Dekang Lv, Xiaobin Wang, Ruicong Wang, Xiaodong Li
Summary: This study systematically analyzed the survival-related AS signal in ovarian serous cystadenocarcinoma and established a new comprehensive prognostic model based on seven AS events. The models were highly efficient in distinguishing patient survival and showed higher prediction ability than mRNA signature, which could be used as potential predictor and therapeutic target for patients with OV.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yalan Luo, Yuyuan Li, Peng Ge, Kaina Zhang, Huanhuan Liu, Nan Jiang
Summary: QKI is found to be reduced in human cervical cancer, and its overexpression inhibits cell proliferation and promotes apoptosis. Through RNA-seq and qRT-PCR, hundreds of QKI-regulated alternative splicing events and differentially expressed genes were identified, closely related to cancer, apoptosis, and transcriptional regulation functions. In conclusion, QKI may impact the occurrence and development of cervical cancer by regulating gene expression through alternative splicing.
DNA AND CELL BIOLOGY
(2021)
Article
Plant Sciences
Zhen Wang, Yechun Hong, Juanjuan Yao, Huan Huang, Bilian Qian, Xue Liu, Yunjuan Chen, Jia Pang, Xiangqiang Zhan, Jian-Kang Zhu, Jianhua Zhu
Summary: Cold stress inhibits plant growth and crop production, but the molecular mechanisms of chilling stress responses in plants are not well understood. This study identified alleles mutants in the SmEb gene that are defective in development and responses to chilling stress. The SmEb gene controls the splicing of pre-mRNAs under chilling stress, which is critical for proper plant development and chilling stress responses.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Yingli Zhong, Jiyong Xie, Suzhen Wen, Wenwu Wu, Li Tan, Mingguang Lei, Huazhong Shi, Jian-kang Zhu
PLANT MOLECULAR BIOLOGY
(2020)
Article
Biology
Chang Zhang, Lei Shen, Wei Yuan, Yuguo Liu, Ruochen Guo, Yangjun Luo, Zheng Zhan, Zhiqin Xie, Guohao Wu, Wenwu Wu, Ying Feng
COMMUNICATIONS BIOLOGY
(2020)
Article
Cell & Tissue Engineering
Yuguo Liu, Yangjun Luo, Lei Shen, Ruochen Guo, Zheng Zhan, Ningyang Yuan, Rula Sha, Wenju Qian, Zhenzhen Wang, Zhiqin Xie, Wenwu Wu, Ying Feng
Article
Plant Sciences
Xiaona Cui, Kaili Gao, Linjuan Wang, Mengyang Lv, Ziwen Li, Donghua Zheng, Wenwu Wu, Wen Yao, Liying Ding, Xiao Li, Jian-Kang Zhu, Hairong Zhang
Summary: AtGCN1 plays a crucial role in gene expression and translation in Arabidopsis, affecting flower development, seed growth, and various physiological processes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Xijuan Zhao, Lingling Tan, Shuo Wang, Yirong Shen, Liangyu Guo, Xiaoxue Ye, Shenkui Liu, Ying Feng, Wenwu Wu
Summary: This study identified 24 PtSR genes in Popolus trichocarpa, showing their constitutive expression in roots, stems, and leaves, and their response to various stresses. PtSCL30 may act as a negative regulator under cold and salt stress in woody plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Xiaoxue Ye, Xijuan Zhao, Yajun Sun, Meijiao Zhang, Shuang Feng, Aimin Zhou, Wenwu Wu, Shurong Ma, Shenkui Liu
Summary: This study investigates the morphological characteristics and potential molecular mechanisms of different types of buds in dioecious Salix. It reveals the development dynamics, gene expression differences, and dynamic changes in sex determination mechanisms of flower buds and leaf buds. The study provides new insights into the molecular mechanisms of dioecious buds and their development, dormancy breaking, flowering, and sexual association.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Hua Liu, Hongna Shang, Huan Yang, Wenjie Liu, Daisuke Tsugama, Ken-Ichi Nonomura, Aimin Zhou, Wenwu Wu, Tetsuo Takano, Shenkui Liu
Summary: The development of floral organs is regulated by a complex network of homeotic genes, and the signaling of gibberellin (GA) is essential for this process. In this study, researchers discovered that the protein MAC5A, which contains an RNA-binding motif, is involved in the development of sepals, petals, and stamens. MAC5A interacts with RBE, a repressor of AG expression, and is required for normal stamen development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Xiaoxue Ye, Shuo Wang, Xijuan Zhao, Ni Gao, Yao Wang, Yanmei Yang, Ernest Wu, Cheng Jiang, Yuxiang Cheng, Wenwu Wu, Shenkui Liu
Summary: Long non-coding RNAs (lncRNAs) play important roles in regulating gene expression under salt stress. This study identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs, in Populus trichocarpa. It was found that lncRNAs can regulate neighboring genes in a cis-regulatory manner and contribute to distant gene expression in a trans-regulatory manner. Additionally, a specific lncRNA, Ptlinc-NAC72, was shown to regulate the expression and functional roles of homologous genes PtNAC72.A/B under long-term salt stress.
Article
Plant Sciences
Shuo Wang, Yirong Shen, Liangyu Guo, Lingling Tan, Xiaoxue Ye, Yanmei Yang, Xijuan Zhao, Yuqi Nie, Deyin Deng, Shenkui Liu, Wenwu Wu
Summary: This study identified 36 TCP genes in Populus trichocarpa and found that this significant innovation was mainly due to recent whole genome duplication (rWGD) after the divergence from Arabidopsis. The study also showed that the expressions of these genes varied among different plant parts and could be regulated by abiotic stresses. Furthermore, a cold-associated regulatory module was identified, suggesting the neofunctionalization of PtrTCP genes in response to environmental changes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Fuqiang Cui, Xiaoxiao Li, Wenwu Wu, Wenbo Luo, Ying Wu, Mikael Brosche, Kirk Overmyer
Summary: MYB108/BOS1 enhances cell death in the gain-of-function mutant bos1-1 after fungal infection and mechanical wounding. Programmed cell death (PCD) is integral to plant life and required for stress responses, immunity, and development. Our understanding of the regulation of PCD is incomplete, especially concerning regulators involved in multiple divergent processes. The botrytis-susceptible (bos1) mutant of Arabidopsis is highly susceptible to fungal infection by Botrytis cinerea (Botrytis). BOS1 (also known as MYB108) regulates cell death propagation during plant responses to wounding. The bos1-1 allele contains a T-DNA insertion in the 5 '-untranslated region upstream of the start codon. This insertion results in elevated expression of BOS1/MYB108. We used clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease 9 (Cas9) system (CRISPR/Cas9) to create new bos1 alleles with disrupted exons, and found that these lines lacked the typical bos1-1 wounding and Botrytis phenotypes. They did exhibit reduced fertility, as was previously observed in other bos1 alleles. Resequencing of the bos1-1 genome confirmed the presence of a mannopine synthase (MAS) promoter at the T-DNA left border. Expression of the BOS1 gene under control of the MAS promoter in wild-type plants conferred the characteristic phenotypes of bos1-1: Botrytis sensitivity and response to wounding. Multiple overexpression lines demonstrated that BOS1 was involved in regulation of cell death propagation in a dosage-dependent manner. Our data indicate that bos1-1 is a gain-of-function mutant and that BOS1 function in regulation of fertility and Botrytis response can both be understood as misregulated cell death.
Article
Biochemistry & Molecular Biology
Yuqi Nie, Liangyu Guo, Fuqiang Cui, Yirong Shen, Xiaoxue Ye, Deyin Deng, Shuo Wang, Jianhua Zhu, Wenwu Wu
Summary: The study reveals the origin and evolution of C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) and their regulatory network. It shows that CBF/DREB1 is an innovation evolved from tandem duplication-derived DREB III gene and has expanded in ancient and modern plants through gene duplication. The duplication events mainly occurred during periods of significant global temperature decrease and the duplicated CBF/DREB1 genes contributed to the rewiring of the regulatory network for cold tolerance in plants.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Liangyu Guo, Shuo Wang, Yuqi Nie, Yirong Shen, Xiaoxue Ye, Wenwu Wu
Summary: Most eudicot plants did not undergo recent whole-genome duplication (R-WGD), but they were still able to adapt to environmental changes. In this study, researchers found that the AP2/ERF transcription factor family was retained after R-WGDs in some eudicot plants and showed exceptional response to cold stimulation. By comparing plants with and without R-WGD, the study revealed convergent expansions of the AP2/ERF III and IX subfamilies through independent duplications and tandem duplications (TDs) after R-WGDs. These expansions coincided with times of global cooling, particularly around and/or after the Cretaceous-Paleogene (K-Pg) boundary. The co-retention and expansion of AP2/ERF III C-repeat binding factor (CBF) duplicates contributed to rewiring of cold-specific regulatory networks in different eudicot lineages.
PLANT COMMUNICATIONS
(2022)
Article
Plant Sciences
Liangyu Guo, Zhiming Xu, Shuo Wang, Yuqi Nie, Xiaoxue Ye, Xuejiao Jin, Jianhua Zhu, Wenwu Wu
Summary: This study investigates the regulatory networks involved in cold responses in three different species of rosids. It demonstrates that some transcription factors and RNA-binding proteins are conserved in the cold response across rosids, and it reveals a hierarchical regulation of differentially expressed genes and alternative splicing genes. The study also identifies a common enrichment related to circadian rhythm in the cold response pathways in all three studied species.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Thermodynamics
Yang Li, Maolin Yu, Yinming Bai, Zhaoyang Hou, Huijie Zhang, Wenwu Wu
Summary: In this study, heat conductive paths were created on the bearing seat and spindle housing to enhance heat dissipation. The temperature distributions of models with and without heat conductive paths were investigated. It was found that the heat dissipation significantly improved with the use of heat conductive paths, and increasing the number and diameter of paths led to lower internal temperatures and reduced temperature difference.
ADVANCES IN MECHANICAL ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Shuo Wang, Yixian Zhang, Xiaoxue Ye, Yirong Shen, Hua Liu, Xijuan Zhao, Liangyu Guo, Lu Cao, Yunfei Du, Wenwu Wu
Summary: Based on high-throughput sequencing, this study selected 11 representative angiosperm species and examined their transcriptome changes during cold adaptation. The findings provide valuable insights into the conserved and evolutionary mechanisms of angiosperms in response to cold stress.