Article
Agriculture, Multidisciplinary
He-nan Su, Yu-xiang Yuan, Shuang-juan Yang, Xiao-chun Wei, Yan-yan Zhao, Zhi-yong Wang, Liu-yue Qin, Zhi-yuan Yang, Liu-jing Niu, Lin Li, Xiao-wei Zhang
Summary: In this study, PacBio RS II SMRT sequencing was used to analyze the full-length transcriptomes of a clubroot-resistant Chinese cabbage variety. The results identified a large number of genes related to clubroot resistance, providing valuable resources for basic research on clubroot resistance in Chinese cabbage.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
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
Plant Sciences
Lina Shang, Yonghong Zhou, Shiqi Wen, Ke Wang, Yang Li, Meihua Zhang, Hongju Jian, Dianqiu Lyu
Summary: Potato is one of the most important tuber food crops, but cultivated potatoes are susceptible to high temperature, affecting yield. This study identified differentially expressed genes in potato under heat stress and revealed their involvement in temperature signaling, phytohormone, and protein modification. Furthermore, genes related to photoperiodic tuberization, tuber formation, and earliness in potato were identified and verified. The findings of this study provide valuable resources for understanding heat stress response in potato and developing heat-tolerant potato varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
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
Biotechnology & Applied Microbiology
Yiming Wang, Linfei Song, Mengfei Ning, Jiaxiang Hu, Han Cai, Weitao Song, Daoqing Gong, Long Liu, Jacqueline Smith, Huifang Li, Yinhua Huang
Summary: This study identifies alternative splicing events (ASEs) related to fatty liver formation in overfed ducks using full-length transcripts and Illumina RNA-seq data. Differential expression of genes involved in lipid metabolism due to ASEs was observed. This study provides insights into the molecular mechanisms of non-pathogenic fatty liver.
Article
Genetics & Heredity
Sofia Papanikolaou, George K. Bertsias, Christoforos Nikolaou
Summary: Alternative RNA splicing can lead to reduced mRNA translation or production of non-functional proteins, playing a vital role in gene regulation. In patients with Systemic Lupus Erythematosus, extensive changes in transcription dynamics were identified, predominantly involving intron retention events. Functional analysis of alternatively spliced genes revealed associations with metabolism and histone acetylation.
Article
Cell Biology
Jichang Liu, Yadong Wang, Xiaogang Zhao, Kai Wang, Chao Wang, Jiajun Du
Summary: This study reveals the significant association between splicing factors and tumor microenvironment remodeling. Evaluating different splicing factor patterns enhances our understanding of the tumor microenvironment and improves effective immunotherapy strategies.
Article
Cell Biology
Jichang Liu, Yadong Wang, Xiaogang Zhao, Kai Wang, Chao Wang, Jiajun Du
Summary: This study identifies the potential roles of splicing factors in the tumor microenvironment and immune regulation. Different splicing factor patterns were associated with specific immune landscapes and were used to classify patients into immune subtypes with different pharmacogenomic landscapes and cell features. The findings enhance our understanding of the tumor microenvironment and can potentially improve immunotherapy strategies.
Article
Biochemistry & Molecular Biology
Yu Jin, Maxim Ivanov, Anna Nelson Dittrich, Andrew D. L. Nelson, Sebastian Marquardt
Summary: This study identified a long noncoding RNA (FLAIL) in Arabidopsis that is associated with flowering. FLAIL directly interacts with target genes and affects their expression through RNA-DNA interactions and alternative splicing. The findings suggest that lncRNAs can regulate gene expression and organismal development as accessory components of the spliceosome.
Article
Biochemistry & Molecular Biology
Andrea Bast-Habersbrunner, Christoph Kiefer, Peter Weber, Tobias Fromme, Anna Schiessl, Petra C. Schwalie, Bart Deplancke, Yongguo Li, Martin Klingenspor
Summary: The nuclear lncRNA Ctcflos plays a crucial role in thermogenic gene expression during brite adipocyte differentiation, by regulating transcriptional recruitment and alternative splicing to drive brite adipogenesis. This highlights the mechanistic versatility of lncRNAs in effectively regulating key differentiation factors at multiple levels of gene expression to direct cell fate and function.
Article
Biology
Vita Setrajcic Dragos, Vida Stegel, Ana Blatnik, Gasper Klancar, Mateja Krajc, Srdjan Novakovic
Summary: The study validates a new simple and direct method for detecting RNA splicing defects, reclassifying the importance of uncertain variants for patient clinical management, and providing a practical protocol for detecting splicing alterations with deep RNA sequencing.
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
Immunology
Meng Zhao, Jingxin Zhou, Yihu Tang, Mingzhu Liu, Yawei Dai, Hui Xie, Zihao Wang, Liang Chen, Yanhu Wu
Summary: This study investigates the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of mitral valve prolapse (MVP). RNA-seq was performed on peripheral blood mononuclear cells (PBMCs) from MVP patients and healthy individuals. Dysregulated RBPs and their associated RASEs were found to play regulatory roles in MVP development.
FRONTIERS IN IMMUNOLOGY
(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
Biochemical Research Methods
Guangyu Yang, Leslie Cope, Zitong He, Liliana Florea
Summary: This study introduces a toolkit called Jutils for visualizing differential splicing events at the intron level. Jutils is method-agnostic, converting outputs from different tools into a unified representation to create heatmaps, sashimi plots, and Venn diagrams. The tool is lightweight and relies solely on a unified data file for visualizations.
Article
Biochemistry & Molecular Biology
K. Teng, G. Z. Xiao, W. E. Guo, J. B. Yuan, J. Li, Y. H. Chao, L. B. Han
GENETICS AND MOLECULAR RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
K. Teng, Z. H. Chang, G. Z. Xiao, W. E. Guo, L. X. Xu, Y. H. Chao, L. B. Han
GENETICS AND MOLECULAR RESEARCH
(2016)
Article
Plant Sciences
Ke Teng, Penghui Tan, Guozeng Xiao, Liebao Han, Zhihui Chang, Yuehui Chao
PLANT CELL REPORTS
(2017)
Article
Plant Sciences
Ke Teng, Zhihui Chang, Xiao Li, Xinbo Sun, Xiaohong Liang, Lixin Xu, Yuehui Chao, Liebao Han
FRONTIERS IN PLANT SCIENCE
(2016)
Article
Plant Sciences
P. -H Tan, L. Zhang, S. -X. Yin, K. Teng
BIOLOGIA PLANTARUM
(2018)
Article
Multidisciplinary Sciences
Zhihui Chang, Yang Liu, Hui Dong, Ke Teng, Liebao Han, Xunzhong Zhang
Article
Plant Sciences
Ke Teng, Penghui Tan, Weier Guo, Yuesen Yue, Xifeng Fan, Juying Wu
FRONTIERS IN PLANT SCIENCE
(2018)
Article
Biochemistry & Molecular Biology
Lijuan Xie, Ke Teng, Penghui Tan, Yuehui Chao, Yinruizhi Li, Weier Guo, Liebao Han
MOLECULAR GENETICS AND GENOMICS
(2020)
Article
Plant Sciences
Lingyun Liu, Xifeng Fan, Penghui Tan, Juying Wu, Hui Zhang, Chao Han, Chao Chen, Lulu Xun, Weier Guo, Zhihui Chang, Ke Teng
Summary: This study conducted RNA-sequencing analysis to investigate gene function annotation of Carex, established fingerprints of 79 Carex species, and analyzed their genetic characteristics and diversity. Results showed samples from different geographic regions clustered together, and indicated that these markers can be used to study the evolutionary history of Carex and related species, as well as guide future breeding projects.
Article
Plant Sciences
Ke Teng, Penghui Tan, Jin Guan, Di Dong, Lingyun Liu, Yidi Guo, Weier Guo, Yue Yuesen, Xifeng Fan, Juying Wu
Summary: ZjNYC1 gene encodes a chlorophyll b reductase responsible for catalyzing chlorophyll b degradation and maintaining photosystem stability. Overexpression of ZjNYC1 accelerates chlorophyll degradation, promotes senescence, and negatively affects photosystem integrity and functionality.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Ke Teng, Yuesen Yue, Hui Zhang, Hui Li, Lixin Xu, Chao Han, Xifeng Fan, Juying Wu
Summary: ZjPPH plays a crucial role in chlorophyll degradation and senescence, with its overexpression accelerating chlorophyll breakdown and promoting senescence by mainly suppressing PSII and PSI to inhibit photosynthetic efficiency.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Jin Guan, Shuxia Yin, Yuesen Yue, Lingyun Liu, Yidi Guo, Hui Zhang, Xifeng Fan, Ke Teng
Summary: This study presents a full-length reference transcriptome of Zoysia japonica using PacBio single-molecule long-read sequencing for the first time. The results identified numerous novel transcripts and transcription factors, and revealed alternative splicing events and alternative polyadenylation sites in Z. japonica. In addition, the underlying transcriptional mechanism of senescence was explored through bioinformatics analysis.
Article
Biochemistry & Molecular Biology
Lingyun Liu, Ke Teng, Xifeng Fan, Chao Han, Hui Zhang, Juying Wu, Zhihui Chang
Summary: This study successfully obtained the full-length transcriptome information of Pennisetum setaceum cv. 'Rubrum' using a combination of single-molecule long-read and Illumina sequencing, and revealed the molecular mechanism of anthocyanin accumulation. The results provide important baseline information for gene function studies and breeding projects.
PLANT MOLECULAR BIOLOGY
(2022)
Article
Agronomy
Jin Guan, Xifeng Fan, Yuesen Yue, Lixin Xu, Ke Teng, Shuxia Yin
Summary: This study conducted an integrated analysis of chlorophyll fluorescence test (JIP-test) and RNA sequencing (RNA-seq) to investigate leaf senescence in Zoysia japonica. A large number of genes associated with leaf senescence, including DNA transcription factor genes and plant hormone response genes, were identified. Additionally, it was found that leaf senescence inhibits chlorophyll biosynthesis while promoting chlorophyll degradation. These findings contribute to understanding the regulatory mechanism of leaf senescence in Z. japonica.