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
Biochemistry & Molecular Biology
Jihae Shin, Qingbao Ding, Luyang Wang, Yange Cui, Erdene Baljinnyam, Aysegul Guvenek, Bin Tian
Summary: APA is an important aspect of gene expression program critical for defining cell identity. A method named CRISPRpas, which enhances proximal PAS usage, is developed to alter APA isoform abundance. The efficiency of CRISPRpas is influenced by various factors. The study demonstrates the modulation of APA for multiple endogenous genes and highlights the impact of CRISPRpas on gene expression.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Siyao Guo, Shuibin Lin
Summary: mRNA polyadenylation plays a crucial role in regulating mRNA metabolism. Mis-regulation of mRNA polyadenylation is often associated with abnormal gene expression and disease progression. This review summarizes the classical process of mRNA 3'-terminal formation, discusses the mechanisms of poly(A) length control in the nucleus and cytoplasm, reviews the progress in alternative polyadenylation regulation and APA site selection mechanism, and finally summarizes the functional roles of APA in gene expression regulation and diseases including cancers.
Article
Biology
Yang Yang, Anirban Paul, Thao Nguyen Bach, Z. Josh Huang, Michael Q. Zhang
Summary: This study introduced a novel computational framework, SAPAS, to identify APA and its association with cell types using single-cell RNA-seq data. The research revealed cell type-specific APA events that play important roles in synaptic architecture and communication. Additionally, the study found a strong enrichment of heritability for psychiatric disorders and brain traits in altered 3' UTRs and coding sequences of cell type-specific APA events.
Article
Biotechnology & Applied Microbiology
Chao Yan, Yupeng Wang, Tao Lyu, Zhikang Hu, Ning Ye, Weixin Liu, Jiyuan Li, Xiaohua Yao, Hengfu Yin
Summary: This study investigated genome-wide changes of polyadenylation sites under heat and cold stresses in Populus trichocarpa, revealing a comprehensive pattern of polyadenylation responsive to temperature stresses in trees. The results suggest that frequent changes in polyA tails may serve as a mechanism of gene regulation in response to stress, associated with distinct sequence signatures.
Review
Cardiac & Cardiovascular Systems
Jun Cao, Muge N. Kuyumcu-Martinez
Summary: This review discusses the importance of cleavage and polyadenylation in gene expression and function, especially in the context of heart development and cardiovascular diseases. It provides an overview of the impact of alternative polyadenylation on gene regulation and the molecular mechanisms controlling it. The dysregulation of alternative polyadenylation in the heart and its implications in cardiovascular diseases are also explored. Additionally, the review discusses strategies for targeting pre-mRNA to correct aberrant patterns of alternative polyadenylation for the treatment of cardiovascular diseases. Overall, this article is significant for understanding gene regulation at the RNA level and for designing RNA-based tools for cardiovascular disease treatment.
CARDIOVASCULAR RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Lorenzo Gallicchio, Gonzalo H. Olivares, Cameron W. Berry, Margaret T. Fuller
Summary: Alternative cleavage and polyadenylation (APA) is a co-transcriptional RNA processing process that greatly affects gene expression. APA occurs naturally during development and cellular differentiation, and changes in APA are associated with pathological states. The understanding of APA regulation and its impact on gene expression is still incomplete.
Review
Genetics & Heredity
Lu Wei, Eric C. Lai
Summary: The process of APA can alter regulatory capacity and coding potential of genes, leading to the formation of characteristic 3' UTR isoforms in neurons. However, our understanding of APA mechanisms and biology is still limited.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Multidisciplinary
Jianwei Cui, Chengping Li, Xiao Cui, Xueyan Liu, Chaoqun Meng, Guoli Zhou
Summary: The study investigates the role of HO1 in preadipocyte differentiation and finds that the HO1 3'UTR short variant, produced by APA, escapes microRNA inhibition and has a stronger inhibitory effect on preadipocyte differentiation.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Xiaoxiao Yang, Yang Tong, Gerui Liu, Jiapei Yuan, Yang Yang
Summary: Alternative polyadenylation (APA) is recognized as a crucial step in post-transcriptional regulation of eukaryotic genes, with tissue- and cell-type-specific occurrences. However, there is currently no database incorporating cell-type level information on APA. Single-cell RNA-seq technology enables analysis of APA at the cell-type level, and the scAPAatlas provides a comprehensive resource for exploring APA across different cell types and interpreting potential biological functions.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Jing Wu, Ligeng Ma, Ying Cao
Summary: Precursor message RNA needs processing to produce mature RNA. Cleavage and polyadenylation at the 3'-end in mRNA maturation is a crucial step. The poly(A) tail of mRNA is essential for nuclear export, stability, translation efficiency, and subcellular localization. Most genes have multiple mRNA isoforms through alternative splicing (AS) or alternative polyadenylation (APA), increasing transcriptome and proteome diversity. This review highlights recent advances in APA regulation of gene expression and stress responses in plants, suggesting APA as a novel strategy for plant adaptation to environmental changes and stress responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Zhigang Yang, Tao Xu, Tao Xie, Liangliang Yang, Guiping Wang, Yang Gao, Gangming Xi, Xiaobiao Zhang
Summary: This study investigated the role of CDC42EP3 in glioma development and its potential downstream mechanism. It was found that CDC42EP3 overexpression was positively correlated with pathological grading and increased the risk of recurrence. Knocking down CDC42EP3 inhibited cell proliferation and migration while promoting apoptosis. The study also suggested that CDC42EP3 might regulate the expression of CCND1. Overall, CDC42EP3 was found to promote glioma progression through targeting CCND1.
CELL DEATH & DISEASE
(2022)
Article
Biochemistry & Molecular Biology
Isabel Pereira-Castro, Beatriz C. Garcia, Ana Curinha, Ana Neves-Costa, Eduardo Conde-Sousa, Luis F. Moita, Alexandra Moreira
Summary: This study investigates the functional significance of alternative polyadenylation (APA) in the regulation of MCL1 in T cells. The results show that T cell activation leads to an increase in mRNA isoforms with short 3' UTRs resulting from APA, which in turn increases the expression of the shorter pA1 isoform and MCL1 protein levels. The less efficiently translated pA2 isoform is downregulated by miR-17. Depletion of either pA1 or pA2 isoforms causes defects in mitochondria morphology, increased apoptosis, and impaired cell proliferation. APA plays a key role in regulating MCL1 protein levels and is essential for T cell survival.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Genetics & Heredity
Xiuye Wang, Liang Liu, Adam W. Whisnant, Thomas Hennig, Lara Djakovic, Nabila Haque, Cindy Bach, Rozanne M. Sandri-Goldin, Florian Erhard, Caroline C. Friedel, Lars Dolken, Yongsheng Shi
Summary: This study reveals that HSV-1 infection causes widespread changes in host mRNA APA with the involvement of ICP27, leading to intronic polyadenylation and early termination of RNAPII. These changes contribute to altered gene expression patterns and the expression of truncated mRNAs, suggesting a multi-faceted host response to viral infection and cellular stress.
Article
Biochemistry & Molecular Biology
Liang Chen, Wei Dong, Menghao Zhou, Chenlu Yang, Ming Xiong, Gallina Kazobinka, Zhaohui Chen, Yifei Xing, Teng Hou
Summary: This study found that downregulation of PABPN1 gene is associated with bladder cancer, and both overexpression and knockdown of PABPN1 affect the aggressiveness of bladder cancer. PABPN1 regulates multiple pathways, including Wnt signaling, cell cycle, and lipid biosynthesis, which contribute to bladder cancer progression. Therefore, targeting PABPN1 therapeutically may hold promise for bladder cancer patients.
CELL AND BIOSCIENCE
(2023)
Review
Immunology
Wenbin Liu, Guangrui Huang, Hongliang Rui, Jie Geng, Haikun Hu, Yujiao Huang, Guiyang Huo, Baoli Liu, Anlong Xu
Summary: Membranous nephropathy (MN) is a common pattern of glomerular injury in multiple autoimmune responses. Detecting autoantibodies can lead to personalized precision medicine. Further identification of autoantibodies and biomarkers is needed to accurately predict disease prognosis and therapeutic response.
AUTOIMMUNITY REVIEWS
(2022)
Article
Biochemical Research Methods
Yuxiu Sun, Chen Li, Wanchen Yu, Guiyang Huo, Mengmeng Zhu, Pengfei Zhao, Ting Wang, Guangrui Huang, Anlong Xu
Summary: Analyzing the serum proteomic profile of SAPHO patients revealed multiple proteins associated with SAPHO syndrome, with inhibitors of the complement system such as CFH and C4BP up-regulated in the syndrome, potentially playing crucial roles in its pathogenesis.
JOURNAL OF PROTEOMICS
(2022)
Article
Allergy
Jianhua Zhen, Pengfei Zhao, Yini Li, Yanan Cai, Wanchen Yu, Wei Wang, Lu Zhao, Hesong Wang, Guangrui Huang, Anlong Xu
Summary: This study explored changes in the gut microbiota, urine metabolome, and plasma proteome in individuals with allergies. Indole derivatives from tryptophan metabolism may play a key role in the progression of allergies and could be potential therapeutic targets.
JOURNAL OF ASTHMA AND ALLERGY
(2022)
Article
Immunology
Yan Chen, Lingjie Luo, Lisi Deng, Xiaoxue Tian, Shangwu Chen, Anlong Xu, Shaochun Yuan
Summary: The AID/APOBEC family expands in primates to resist viruses and retrotransposons. Recently, expansion of AID/APOBEC-like genes has also been observed in lamprey. The study suggests that the arms race between host and pathogens, along with VLR assembly, may contribute to the expansion and diversification of the lamprey AID/APOBEC family.
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Multidisciplinary Sciences
Xin Tao, Ziwen Huang, Fan Chen, Xinli Wang, Tingting Zheng, Shaochun Yuan, Anlong Xu
NATIONAL SCIENCE REVIEW
(2022)
Article
Biochemistry & Molecular Biology
Liutao Chen, Yonggui Fu, Zhijie Hu, Ke Deng, Zili Song, Susu Liu, Mengxia Li, Xin Ou, Runze Wu, Mian Liu, Rui Li, Shuiying Gao, Lin Cheng, Shangwu Chen, Anlong Xu
Summary: The N6-methyladenosine (m(6)A) modification and alternative polyadenylation (APA) are important regulators of gene expression. YTHDC1, an m(6)A reader, was found to suppress proximal APA sites and produce longer 3' UTR transcripts by binding to upstream m(6)A sites. The interaction between YTHDC1 and FIP1L1, as well as the liquid-liquid phase separation promoted by m(6)A binding, may play a crucial role in APA regulation.
Article
Plant Sciences
Peng Tian, Lili Wu, Maya Kudo, Misa Hayashi, Lingling Qin, Ming Gao, Anlong Xu, Tonghua Liu
Summary: TNK can reduce obesity by regulating intestinal flora and is associated with fatty acid metabolism.
PHARMACEUTICAL BIOLOGY
(2022)
Article
Cell Biology
Zhijie Hu, Mengxia Li, Zhanfeng Huo, Liutao Chen, Susu Liu, Ke Deng, Xin Lu, Shangwu Chen, Yonggui Fu, Anlong Xu
Summary: Alternative splicing and alternative polyadenylation (APA) are crucial for gene regulation in eukaryotic cells. While the U1 snRNP complex can suppress proximal APA sites, the free proteins of this complex actually promote the usage of these sites, indicating a contrasting role.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2022)
Article
Immunology
Jin Li, Shumin Liu, Yang Zhang, Qiuyun Huang, Hao Zhang, Jihua OuYang, Fan Mao, Huiping Fan, Wenjie Yi, Meiling Dong, Anlong Xu, Shengfeng Huang
Summary: The Apextrin C-terminal (ApeC) domain is a protein domain largely specific to aquatic invertebrates. This study examined 130 ACPs from gastropods and bivalves, classifying them into different groups based on their phylogenetics and architectures. The study found that the selected ACPs from bivalves and gastropods showed high affinities to certain types of peptidoglycan, but weak or no affinities to other microbial cell wall components. Furthermore, the ACP from the bivalve had the highest expression in the gill and could be up-regulated after bacterial challenge, similar to the findings in amphioxus ACPs.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Wan-di Feng, Yao Wang, Tong Luo, Xin Jia, Cui-qin Cheng, Hao-jia Wang, Mei-qi Zhang, Qi-qi Li, Xue-jiao Wang, Yi-ying Li, Jin-yong Wang, Guang-rui Huang, Ting Wang, An-long Xu
Summary: Recent evidence suggests that targeting NLRP3 inflammasome activation is important for treating inflammasome-driven diseases. Scoparone, a natural compound from the Chinese herb Artemisia capillaris Thunb, has anti-inflammatory activity. This study investigated the effect of scoparone on NLRP3 inflammasome activation in inflammatory diseases.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Oncology
Ying Shi, Xiaopu Sang, Jiali Deng, Yihang Wang, Xiaoni Chen, Shan Lin, Fenfang Wu, Anlong Xu
Summary: This study found that cell cycle-related genes play a key role in the development and prognosis of hepatocellular carcinoma (HCC), and are significantly correlated with immune cell infiltration. The expression levels of CDK1, CDC20, CCNA2, CCNB1, and CCNB2 may be involved in the regulation of monocytes and tumor-associated macrophages (TAMs) in HCC. These findings suggest that cell cycle-related genes can be used as novel biomarkers for exploring the prognosis and immune cell infiltration of HCC.
Article
Cell & Tissue Engineering
Ying Shi, Jiali Deng, Xiaopu Sang, Yihang Wang, Fei He, Xiaoni Chen, Anlong Xu, Fenfang Wu
Summary: By including BMP4 in the hepatic differentiation medium, we have achieved co-differentiation of endoderm-derived hepatocytes and mesoderm-derived nonparenchymal cells, which has a beneficial effect on hepatocyte maturation and lifespan in vitro.
STEM CELLS INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Zirui Yue, Zhaoyu Fan, Hao Zhang, Buhan Feng, Chengyi Wu, Shenghui Chen, Jihua Ouyang, Huiping Fan, Panwei Weng, Huixiong Feng, Shangwu Chen, Meiling Dong, Anlong Xu, Shengfeng Huang
Summary: The chitin-based peritrophic matrix (PM), which was traditionally believed to be lost in vertebrates, has been discovered in fishes as a chitinous membrane (CM). In zebrafish, the CM plays a role in ingestion behavior, microbial homeostasis, epithelial renewal, digestion, growth, and longevity. Although not essential for gut immunity, the CM may provide insights into the understanding of vertebrate gut physiology and human intestinal diseases.
Article
Cell Biology
Susu Liu, Runze Wu, Liutao Chen, Ke Deng, Xin Ou, Xin Lu, Mengxia Li, Chao Liu, Shangwu Chen, Yonggui Fu, Anlong Xu
Summary: CPSF6 undergoes liquid-liquid phase separation (LLPS) to regulate alternative polyadenylation in cancer cells. CLK2 kinase disrupts CPSF6 LLPS, affecting the length of 3'UTRs of cell-cycle-related genes and cell proliferation.
Article
Biochemistry & Molecular Biology
Hongmei Li, Fenfang Wu, Guangrui Huang, Di Wu, Ting Wang, Xiashuang Wang, Kai Wang, Yuyin Feng, Anlong Xu
Summary: Recent studies have shown that transplantation of hiPS-CMs is a promising approach for treating heart failure, but the immature nature and secreted proteins of hiPS-CMs involved in cardiomyocyte repair are not well understood. In this study, a saponin(+) compound induced system was established to generate stable and functional hiPS-CMs in vitro and transplanted into heart failure mice. The results demonstrated that the optimally induced hiPS-CMs had enhanced therapeutic effects by reducing cardiac remodeling and dysfunction, decreasing cardiomyocyte death, and promoting angiogenesis. The reparative effect was likely mediated by the secretion of PDGF-BB and the activation of the PI3K/Akt pathway.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)