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
Plant Sciences
Ping Lu, Daipeng Chen, Zhaomei Qi, Haoming Wang, Yitong Chen, Qinhu Wang, Cong Jiang, Jin-Rong Xu, Huiquan Liu
Summary: This study investigates the landscape and regulation of alternative splicing (AS) and alternative polyadenylation (APA) in Fusarium graminearum, a filamentous fungus. The results reveal that AS and APA play important roles in gene expression regulation, with the majority of AS events affecting coding sequences. Unexpectedly, AS transcripts with premature-termination codons are not degraded. Distal APA sites have strong signals, while proximal APA isoforms are highly expressed in F. graminearum. The study also uncovers the roles of 3'-end processing factors in promoting proximal APA site usage and intron splicing. Furthermore, the study suggests intron inclusion and 3'-untranslated region lengthening as novel mechanisms in regulating aging and dormancy in fungi.
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
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.
Review
Immunology
Davia Blake, Kristen W. Lynch
Summary: The latest advances in next-generation sequencing studies have revealed a high frequency of genes regulated by RNA processing mechanisms in the immune system, particularly alternative splicing and alternative polyadenylation. These mechanisms have the potential to alter protein identity, control protein abundance, localization, and association with other factors. This review focuses on how control of apoptosis by alternative splicing and alternative polyadenylation is utilized to tune cell fate during an immune response.
IMMUNOLOGICAL REVIEWS
(2021)
Article
Genetics & Heredity
Leonard Scharfen, Dagmar Zigackova, Kirsten A. Reimer, Martha R. Stark, Viktor A. Slat, Nancy J. Francoeur, Melissa L. Wells, Lecong Zhou, Perry J. Blackshear, Karla M. Neugebauer, Stephen D. Rader
Summary: By studying a highly diverged red alga, researchers discovered the presence of alternative polyadenylation (APA) in this non-model organism, suggesting its potential importance in regulating gene expression.
FRONTIERS IN GENETICS
(2022)
Article
Immunology
Sanqi An, Yueqi Li, Yao Lin, Jiemei Chu, Jinming Su, Qiuli Chen, Hailong Wang, Peijiang Pan, Ruili Zheng, Jingyi Li, Junjun Jiang, Li Ye, Hao Liang
Summary: The study found that genes with APA in COVID-19 patients were enriched in gene ontology categories related to innate immunity, and APA events may provide better predictions than AS. This suggests that APA could act as a potential therapeutic target and novel biomarker in COVID-19 patients.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kun Ma, Jingluan Han, Zixu Zhang, Heying Li, Yanchang Zhao, Qinlong Zhu, Yongyao Xie, Yao-Guang Liu, Letian Chen
Summary: N-6-methyladenosine (m(6)A)) modification plays a crucial role in post-transcriptional regulation of eukaryotic gene expression, with OsEDM2L identified as a key protein essential for rice anther development through regulating the m(6)A modification of EAT1 mRNA to impact tapetal programmed cell death.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Review
Plant Sciences
Jiaying Zhu, Changhao Li, Xu Peng, Xiuren Zhang
Summary: RNA secondary structure (RSS) is crucial in various biological processes, including RNA processing, transportation, and translation, as well as plant responses to environmental variations. At the molecular level, RSS is correlated with splicing, protein synthesis, and miRNA biogenesis.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Plant Sciences
Varvara Dikaya, Nabila El Arbi, Nelson Rojas-Murcia, Sarah Muniz Nardeli, Daniela Goretti, Markus Schmid
Summary: Alternative splicing in plants is closely linked to their ability to perceive environmental stimuli, particularly temperature, which strongly influences plant development and morphology.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Momoko Ohori, Yusuke Nakayama, Mari Ogasawara-Shimizu, Hiroyoshi Toyoshiba, Atsushi Nakanishi, Samuel Aparicio, Shinsuke Araki
Summary: This study provides a comprehensive description of the transcriptome landscape of replicative senescent human umbilical vein endothelial cells, identifying key genes and pathways involved in age-related processes such as lipid metabolism and chromosome organization. The research also reveals the involvement of alternative splicing in endothelial cell senescence.
Article
Plant Sciences
Xinhui Xia, Minhong Fan, Yuqi Liu, Xinyue Chang, Jingting Wang, Jingjing Qian, Yuchen Yang
Summary: Dwarfed stature is a desirable trait in pomegranate cultivation. This study investigates the role of alternative polyadenylation (APA) in regulating plant growth-related genes and the overall growth and development of pomegranate seedlings under plant growth retardant (PGR) treatments. APA was found to regulate the transcriptome through microRNA-mediated mRNA cleavage or translation inhibition, leading to changes in the expression of genes associated with developmental growth, lateral root branching, and shoot apical meristem maintenance. These findings provide new insights into the genetic basis of pomegranate growth and development.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Pui Ying Lam, Lanxiang Wang, Clive Lo, Fu-Yuan Zhu
Summary: Plant metabolism plays a crucial role in plant survival, growth, development, and interaction with the environment. It is tightly regulated at transcriptional, post-transcriptional, translational, and post-translational levels in response to different growth stages and changing environment. Alternative splicing, a post-transcriptional regulatory mechanism, generates multiple protein isoforms from a single gene and regulates plant metabolism by altering biochemical activities, protein interactions, and subcellular localization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Xue Yang, Zichang Jia, Qiong Pu, Yuan Tian, Fuyuan Zhu, Yinggao Liu
Summary: This paper briefly introduces the mechanism of ABA-induced alternative splicing and the role of ABA mediating AS in plant response to the environment and its own growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Ning Wang, Yue Hu, Zefeng Wang
Summary: Eukaryotic gene expression is tightly regulated at multiple levels, including alternative splicing, which generates multiple mRNA isoforms from a single gene. Epigenetic modifications play crucial roles in the regulation of alternative splicing by affecting transcription, splicing factor recruitment, and splicing factor expression/activity. Dysregulation of epigenetics and splicing is common in cancer and can have functional consequences. Understanding the complex regulation of gene expression layers can provide new insights into modulating disease-related splicing dysregulation.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Biochemistry & Molecular Biology
Congting Ye, Qian Zhou, Yiling Hong, Qingshun Quinn Li
Article
Biochemical Research Methods
Congting Ye, Qian Zhou, Xiaohui Wu, Chen Yu, Guoli Ji, Daniel R. Saban, Qingshun Q. Li
Article
Environmental Sciences
Congting Ye, Qian Zhou, Xiaohui Wu, Guoli Ji, Qingshun Quinn Li
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2019)
Article
Biochemistry & Molecular Biology
Juncheng Lin, Fu-Yu Hung, Congting Ye, Liwei Hong, Yuan-Hsin Shih, Keqiang Wu, Qingshun Q. Li
Editorial Material
Ecology
Yuan-Ye Zhang, Junjie Yin, Ming Zhou, Zeru Lin, Qingshun Q. Li
Article
Biochemistry & Molecular Biology
Juncheng Lin, Zhibo Yu, Congting Ye, Liwei Hong, Yiru Chu, Yingjia Shen, Qingshun Q. Li
Summary: The study reveals that alternative polyadenylation can affect the 3' end profile of transcripts in Arabidopsis, indicating significant differences in expression and translation activity between rhythmic and arrhythmic transcripts. Additionally, rhythmic transcripts contain a higher proportion of AAUAAA and UGUA signals.
Article
Pharmacology & Pharmacy
Hao Li, Qingshun Q. Li, Yiling Hong
Summary: Studies have shown that silver nanoparticles have adverse effects on human neural development, including inhibition of neural progenitor proliferation and neurite outgrowth, promotion of astrocyte activation and neuronal apoptosis. Supplementation with ascorbic acid can partially restore these adverse effects.
Article
Biology
Zhaoyang Liu, Amro A. Hussien, Yunjia Wang, Terry Heckmann, Roberto Gonzalez, Courtney M. Karner, Jess G. Snedeker, Ryan S. Gray
Summary: This study demonstrates the essential role of the ADGRG6 gene in maintaining spinal alignment and regulating biomechanical properties of tendons and gene expression in cartilaginous tissues. The findings suggest novel therapeutic opportunities for human scoliosis by targeting core pathways regulated by ADGRG6.
Article
Ecology
Junjie Yin, Xiaohe Lin, Jing Yao, Qingshun Q. Li, Yuan-Ye Zhang
Summary: This study used natural variation in Arabidopsis thaliana to explore transgenerational effects in response to drought and nutrient addition. The results showed that transgenerational plasticity depended on the offspring environment and genotype, with greater transgenerational plasticity observed in genotypes from locations with greater temporal autocorrelation of annual temperature and precipitation. These findings suggest that the evolution of transgenerational effects is not random and may be influenced by the predictability of natural environments.
Review
Plant Sciences
Juncheng Lin, Qingshun Quinn Li
Summary: Precise regulation of gene expression is essential for plant survival. Pre-mRNA polyadenylation, as a cotranscriptional regulatory mechanism, plays a crucial role in fine-tuning gene expression. Epigenetic modification, including DNA methylation, histone modifications, and epitranscriptomic modification, has been found to be involved in regulating polyadenylation in plants. This article summarizes the links between epigenetics and polyadenylation and discusses their novel biological efficacy for plant development and environmental responses.
TRENDS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Hui Ma, Juncheng Lin, Fangming Mei, Hude Mao, Qingshun Q. Li
Summary: The expression of homoeologous genes in allohexaploid wheat genome remains largely unknown at the co-transcriptional level. This study focused on alternative polyadenylation (APA) and found that drought stress led to extensive APA in wheat, involving a large number of stress-responsive genes. The study also revealed different poly(A) sites, APA patterns, and 3' UTR length changes among homoeologous genes. These findings shed light on the role of APA in drought stress response and provide new insights into the adaptability of homoeologous genes through transcriptome diversity.
Article
Plant Sciences
Saiqi Hao, Lidan Zhang, Danhui Zhao, Jiawen Zhou, Congting Ye, Haidong Qu, Qingshun Q. Li
Summary: CPSF is a protein complex involved in mRNA 3'end formation, but its biological functions in multicellular eukaryotes are mostly unknown. Through studying AtCPSF73 in Arabidopsis, it was found that it plays a critical role in regulating gene expression and poly(A) site choice, which affects plant growth and development.
Review
Plant Sciences
Jiawen Zhou, Qingshun Quinn Li
Summary: Alternative polyadenylation (APA) is an important mechanism for plants to regulate gene expression by increasing transcriptome diversity and plasticity. This study reviews the dynamic features and consequences of APA in plants subjected to both biotic and abiotic stresses, and proposes a general APA model that reveals the mechanisms of APA in modulating gene expression during stress response in plants.
MOLECULAR HORTICULTURE
(2023)
Article
Forestry
Saiqi Hao, Wei Hu, Congting Ye, Yingjia Shen, Qingshun Q. Li
Summary: The study investigated the development of propagule plastids in woody plants using Kandelia obovata as a model species. Albino propagules with etioplasts and reduced photosynthesis rates were identified, and a genome-wide association study identified significant single nucleotide polymorphisms associated with propagule plastid development. Differentially expressed genes related to porphyrin and chlorophyll metabolisms, carotenoid and flavonoid biosynthesis were also identified. The study shed light on the genetic mechanisms regulating propagule plastid development in woody plants.
Article
Biochemistry & Molecular Biology
Nadja Makki, Jingjing Zhao, Zhaoyang Liu, Walter L. Eckalbar, Aki Ushiki, Anas M. Khanshour, Joe Wu, Jonathan Rios, Ryan S. Gray, Carol A. Wise, Nadav Ahituv
HUMAN MOLECULAR GENETICS
(2020)