Article
Plant Sciences
Zhongxin Jin, Xinning Lv, Yushuai Sun, Zongbao Fan, Guangqing Xiang, Yuxin Yao
Summary: The study identified a total of 8,453 AS events in grapevine roots, with retained intron (RI) being the most dominant type, and showed a global decrease in inclusion isoforms proportion under salt stress. Only a small overlap was found between salt-responsive AS events and differentially expressed genes, while differentially spliced genes were mainly related to RNA processing, nucleic acid binding, and ion channel activity. Additionally, the study identified salt-induced spliceosomal protein genes LSM2 and SRSF1 in grapevine roots and proposed a method to explore interactions between AS and alternative polyadenylation (APA) using Iso-Seq data.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Multidisciplinary Sciences
Junliang Wang, Wei Chen, Wenjun Yue, Wenhong Hou, Feng Rao, Hanbing Zhong, Yuanming Qi, Ni Hong, Ting Ni, Wenfei Jin
Summary: This study developed a single-cell polyadenylation sequencing method to investigate the landscape of alternative polyadenylation (APA) at the single-cell level. The results showed that genes with multiple polyA sites in bulk data tend to use only one site in each single cell. Cell cycle genes were found to have high variation in polyA site usages. Furthermore, polyA site usage switch played an important role in cell cycle regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Neurosciences
Mohammad-Erfan Farhadieh, Kamran Ghaedi
Summary: Alzheimer's disease is a neurodegenerative disease that affects the brain's cells, leading to memory loss and changes in behavior and language skills. This study analyzes alternative splicing events at the cellular level in postmortem brain tissue, revealing previously overlooked changes in splicing and expression in AD patient brains. The findings indicate that specific cell types exhibit splicing changes associated with AD, providing valuable insights into the disease's pathology.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Cheng-Yan Mou, Qiang Li, Zhi-Peng Huang, Hong-Yu Ke, Han Zhao, Zhong-Meng Zhao, Yuan-Liang Duan, Hua-Dong Li, Yu Xiao, Zhou-Ming Qian, Jun Du, Jian Zhou, Lu Zhang
Summary: This study generated a full-length transcriptome of oriental river prawn muscle using the PacBio Sequel platform, and identified 6,599 error-corrected isoforms. Transcriptome structural analysis revealed thousands of alternative splicing and polyadenylation events. This study provides valuable information for understanding the genomic structure and improving the genome annotation of oriental river prawn.
Article
Biochemistry & Molecular Biology
Shuang-Yan Zheng, Lu-Xia Pan, Fu-Ping Cheng, Meng-Jie Jin, Zi-Long Wang
Summary: In this study, the full-length transcriptome of A. mellifera was sequenced using PacBio technology. A total of 116,535 transcripts and 30,045 genes were identified. Compared to the reference genome, 18,915 gene loci and 96,176 transcripts were newly identified. Additionally, alternative splicing events, alternative polyadenylation sites and long non-coding RNAs were detected. These findings expand our understanding of the complexity and diversity of the honey bee transcriptome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Joana Wilton, Filipa Lopes de Mendonca, Isabel Pereira-Castro, Michael Tellier, Takayuki Nojima, Angela M. Costa, Jaime Freitas, Shona Murphy, Maria Jose Oliveira, Nicholas J. Proudfoot, Alexandra Moreira
Summary: In this study, new 3'UTR-APA and IPA mRNA isoforms were found during pro-inflammatory polarization of primary human macrophages and CRC co-culture, which may be used as diagnostic or therapeutic tools in the future.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yongtao Yu, Yuxiang Liufu, Yi Ren, Jie Zhang, Maoying Li, Shouwei Tian, Jinfang Wang, Shengjin Liao, Guoyi Gong, Haiying Zhang, Shaogui Guo
Summary: This study used PacBio single-molecule long-read sequencing to identify alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. The results showed that these post-transcriptional mechanisms play important roles in fruit ripening, particularly the splicing isoforms associated with fruit ripening. Additionally, KEGG analysis revealed that fructose and mannose metabolism, starch and sucrose metabolism, and carotenoid biosynthesis were enriched in genes undergoing AS and APA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Shi-lu Chen, Zhong-xu Zhu, Xia Yang, Li-li Liu, Yang-fan He, Ming-ming Yang, Xin-yuan Guan, Xin Wang, Jing-ping Yun
Summary: APA plays a crucial role in HCC, with CPSF1 identified as a key regulator contributing to unfavorable survival outcomes in HCC. Knockdown of CPSF1 inhibits HCC cell proliferation and migration, while overexpression has the opposite effect. Knockdown of CPSF1 not only induces APA but also increases AS events.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Carmelo Gurnari, Simona Pagliuca, Valeria Visconte
Summary: Alternative RNA splicing is an essential physiological function that plays a crucial role in cellular development. RNA splicing dysfunction has been implicated in the development of several cancers, including myeloid malignancies. Cancer cells exhibit marked gene expression alterations, including different usage of AS isoforms, potentially causing tissue-specific effects and disruptions of downstream pathways.
Article
Biochemistry & Molecular Biology
Rebecca M. Sena, Jeffery L. Twiss, Amy S. Gardiner, Michela Dell'Orco, David N. Linsenbardt, Nora Perrone-Bizzozero
Summary: Neuronal Hu/ELAV-like proteins HuB, HuC, and HuD play key roles in the proper development and maintenance of the nervous system by regulating mRNA stability, transport, translation, as well as alternative splicing and polyadenylation. Deletion of HuD has a greater impact on alternative splicing with 310 genes affected, although it also influences polyadenylation of 53 genes. This study provides insights into the transcriptomic effects of HuD deletion on nuclear events in the neocortex.
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
Genetics & Heredity
Zhen Zhu, Shuangying Ni, Jiali Zhang, Ying Yuan, Yun Bai, Xueli Yin, Zhengwei Zhu
Summary: This study analyzed RNA-Seq data to identify differential alternative splicing events associated with trauma healing in keloid-prone individuals (KPIs) and healthy controls (HCs). Functional differences were also analyzed, and the co-expression relationship of differentially alternative splicing genes and RNA binding proteins (RBPs) was established. The results provide insights into the regulation of wound healing in KPIs and HCs.
FRONTIERS IN GENETICS
(2023)
Review
Endocrinology & Metabolism
Panyisha Wu, Moya Zhang, Nicholas J. G. Webster
Summary: Alternative RNA splicing is an important biological process that has been linked to various clinical syndromes, but its applicability to common diseases is still uncertain. This review focuses on the changes in alternative RNA splicing in fatty liver disease and the role of splicing regulation in disease progression.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Jun Sun, Zhe Liu, Jinqiang Quan, Lanlan Li, Guiyan Zhao, Junhao Lu
Summary: In this study, RNA transcriptome sequencing technology (RNA-Seq) and genomic information were used to identify alternative splicing events in rainbow trout, revealing a large number of differential alternative splicing events and differentially expressed genes under heat stress. Gene ontology and pathway enrichment analysis showed the gene expression characteristics of rainbow trout under heat stress. The results were validated by qRT-PCR, confirming the reliability of the bioinformatics analysis.
MARINE BIOTECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Lulu Yu, Vladimir Majerciak, Zhi-Ming Zheng
Summary: Human papillomaviruses (HPV) are a group of viruses that cause cancer, with HPV16 and HPV18 being the most common types responsible for majority of cases. The expression of their genome is regulated by alternative RNA splicing, and epigenetic modifications also play a role in HPV infections and carcinogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Si Wu, Mei Ying Yang, Meng Long Fan, Ying Zhang, Xin Lei Li, Heng Fu Yin, Ji Yuan Li
Summary: This study discovered the complete chloroplast genome of Camellia confusa and identified 130 genes within. Phylogenetic analysis revealed the close relationship between C. confusa and C. meiocarpa. These findings provide valuable information for the study of camellia evolution.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Plant Sciences
Menglong Fan, Xinlei Li, Ying Zhang, Si Wu, Zhixin Song, Hengfu Yin, Weixin Liu, Zhengqi Fan, Jiyuan Li
Summary: In this study, a comprehensive comparative transcriptome analysis was performed to identify the key pathways and genes involved in the regulation of double flower patterns in Camellia sasanqua. Differential gene expression analysis revealed the importance of plant hormone signaling and secondary metabolites in double flower formation. The study also validated the ABCE model and found that the expansion of class A gene activity influenced the formation of double flowers.
Article
Forestry
Junling Wang, Xijian Fan, Xubing Yang, Tardi Tjahjadi, Yupeng Wang
Summary: This paper proposes a semi-supervised learning-based segmentation network, SemiFSNet, which enhances model performance through occlusion-aware data augmentation, dynamic convolution, and attention mechanism, as well as exploiting rich information from unlabeled data using consistency regularization to effectively monitor forest fires.
Article
Biochemistry & Molecular Biology
Ping Lin, Hengfu Yin, Kailiang Wang, Haidong Gao, Lei Liu, Xiaohua Yao
Summary: In this study, the chloroplast genome sequences of nine Camellia species were determined using Illumina sequencing technology. Comparative analysis revealed high sequence polymorphism and identified specific sequence markers for species identification and phylogenetic analysis. Additionally, regional constraints were found to strongly influence the sequence evolution of the chloroplast genomes.
Article
Biochemistry & Molecular Biology
Menglong Fan, XinLei Li, Ying Zhang, Meiying Yang, Si Wu, HengFu Yin, WeiXin Liu, ZhengQi Fan, JiYuan Li
Summary: This study characterized the anthocyanin profile of 20 C. sasanqua cultivars and revealed the regulatory mechanism of color diversity in this plant. Through transcriptome analysis, candidate genes and transcription factors involved in anthocyanin biosynthesis were identified. The findings provide valuable resources for studying flower color in C. sasanqua and for genetic modification of anthocyanin biosynthesis.
PLANT MOLECULAR BIOLOGY
(2023)
Review
Plant Sciences
Zhiguo Shen, Xin Ding, Jianming Cheng, Fangfang Wu, Hengfu Yin, Minyan Wang
Summary: Magnoliids are a major clade of flowering plants that have great economic and ecological values. The evolutionary status of magnoliids has become a hot topic in plant phylogenetic research due to the accumulation of genomic information. However, current studies on the phylogenetic status of magnoliids have produced inconsistent results.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Suhang Yu, Jiyuan Li, Ting Peng, Sui Ni, Yi Feng, Qiushi Wang, Minyan Wang, Xian Chu, Zhengqi Fan, Xinlei Li, Hengfu Yin, Wanchuan Ge, Weixin Liu
Summary: In this study, a new member of the chalcone isomerase (CHI) gene family, CnCHI4, was identified in Camellia nitidissima. CnCHI4 plays an important role in the biosynthesis pathway of flavonoids and its function is regulated by the transcription factor CnMYB7.
Article
Forestry
Jianhua Dai, Yanru Fan, Shu Diao, Hengfu Yin, Xiaojiao Han, Jun Liu
Summary: This study analyzed the genetic diversity and core gene pool of T. sinensis and established a comprehensive evaluation method, resulting in the identification of a best core collection and the screening of superior individual plants. These findings will contribute to the preservation and utilization of T. sinensis germplasm resources, as well as the improvement of T. sinensis varieties.
Article
Plant Sciences
Xianjin Ma, Ziyan Nie, Hu Huang, Chao Yan, Sijia Li, Zhikang Hu, Yupeng Wang, Hengfu Yin
Summary: This study identified a small regulatory RNA, cja-miR5179, which is exclusively expressed in the ovules of Camellia japonica during early floral development. The miRNA targets a B-class MADS-box gene and its regulation is conserved between Camellia and orchids. The study highlights the evolutionary conservation and functional divergence of small RNAs in floral development.
Article
Computer Science, Artificial Intelligence
Fa Zhu, Wenjie Zhang, Xingchi Chen, Xizhan Gao, Ning Ye
Summary: As a state-of-the-art supervised novelty detection model, SVM-SND can recognize novelty or the class of a test instance through a single model. However, maximizing minimum margin is not sufficient for ensuring classification generalization. This paper introduces margin distribution and proposes an LMD-SND model to enhance the performance of multi-class supervised novelty detection. Experimental results show that LMD-SND outperforms SVM-SND and achieves comparative performance with shallow and deep novelty detection models.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Physics, Multidisciplinary
Jianghui Sang, Zaki Ahmad Khan, Hengfu Yin, Yupeng Wang
Summary: This paper proposes a novel approach called phi DCN, which extends undirected graph convolution to directed graphs and utilizes the directed graph Laplacian to propagate messages for potential-based reward shaping. Experimental results show that phi DCN exhibits a substantial improvement compared to other algorithms on both Atari and MuJoCo benchmarks.
FRONTIERS IN PHYSICS
(2023)
Article
Horticulture
Menglong Fan, Ying Zhang, Meiying Yang, Si Wu, Hengfu Yin, Jiyuan Li, Xinlei Li
Summary: This study investigates the molecular mechanism of flower color variations in Camellia japonica caused by bud sport. The researchers identified anthocyanins as the main factors affecting petal redness and identified potential co-expression modules and differentially expressed genes related to anthocyanin accumulation. Integrated analysis suggests that CjMYB62, CjMYB52, and CjGATA may play important roles in anthocyanin accumulation.
Article
Biochemistry & Molecular Biology
Xianjin Ma, Yifan Yu, Zhikang Hu, Hu Huang, Sijia Li, Hengfu Yin
Summary: The developmental regulation of flower organs involves the spatio-temporal regulation of floral homeotic genes. BASIC PENTACYSTEINE genes (BPC genes) are plant-specific transcription factors that play important roles in plant development. In this study, a Class I BPC gene (CjBPC1) from Camellia japonica was characterized. It was found that CjBPC1 is highly expressed in the central whorls of flowers and overexpression of it in Arabidopsis led to severe defects in siliques and seeds. Further analysis revealed that CjBPC1 recruits the Polycomb Repression Complex to suppress the expression of genes involved in ovule and seed development.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Horticulture
Sijia Li, Hu Huang, Xianjin Ma, Zhikang Hu, Jiyuan Li, Hengfu Yin
Summary: Through genome-wide characterization and expression profiling, we investigated the regulatory roles of MYB family genes in seed oil biosynthesis in Camellia oleifera. We identified potential regulators and discovered the importance of tandem duplications in the expansion of the MYB subfamily. Furthermore, we revealed MYB genes potentially involved in lipid metabolism and seed maturation.
Article
Biotechnology & Applied Microbiology
Ping Lin, Kailiang Wang, Yupeng Wang, Zhikang Hu, Chao Yan, Hu Huang, Xianjin Ma, Yongqing Cao, Wei Long, Weixin Liu, Xinlei Li, Zhengqi Fan, Jiyuan Li, Ning Ye, Huadong Ren, Xiaohua Yao, Hengfu Yin
Summary: This study establishes a chromosome-scale reference genome for oil-Camellia plants and reveals the genetic and genomic basis of oil-Camellia domestication. Artificial selection of genes involved in oil biosynthesis and phytohormone pathways contributes to improving the yield and quality of seed oil in oil-Camellia.