Article
Biochemical Research Methods
Xiaohui Wu, Tao Liu, Congting Ye, Wenbin Ye, Guoli Ji
Summary: APA plays a crucial role in transcriptome diversity and gene expression regulation. The newly developed tool scAPAtrap can accurately identify poly(A) sites at the whole genome level in individual cells, even for sites with low read coverage, without relying on priori genome annotation. Compared to existing methods, scAPAtrap shows higher accuracy and sensitivity in identifying poly(A) sites, making it a valuable tool for exploring APA dynamics and heterogeneous APA isoform expression at the single-cell level.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Lingwu Qian, Hongjuan Fu, Yunwen Mou, Weixu Lin, Lishan Ye, Guoli Ji
Summary: In this study, we proposed an analysis framework called scAPAmod to accurately identify patterns of APA usage at the single-cell level. We used scAPAmod to analyze the dynamic changes in APA usage patterns during mouse spermatogenesis and identified cell-type-specific APA usage patterns. This study provides a higher resolution analysis of single-cell gene expression heterogeneity compared to traditional gene expression profiling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Biochemical Research Methods
Naima Ahmed Fahmi, Khandakar Tanvir Ahmed, Jae-Woong Chang, Heba Nassereddeen, Deliang Fan, Jeongsik Yong, Wei Zhang
Summary: Research has shown that alternative polyadenylation (APA) can regulate gene expression; current bioinformatics pipelines have limitations in analyzing 3'-UTR APA events; APA-Scan is a powerful program that can detect 3'-UTR APA events and provide high-resolution results.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Miguel Barquin, Ian U. Kouzel, Beat Ehrmann, Michael Basler, Andreas J. Gruber
Summary: This study presents a single cell-based Terminal Exon Annotation database (scTEA-db), which provides yet unannotated terminal exons and associated transcript isoforms for studying their biological role in cell identity and function.
NUCLEIC ACIDS RESEARCH
(2023)
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)
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Review
Biochemistry & Molecular Biology
Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David R. Powell, Traude H. Beilharz
Summary: Alternative transcript cleavage and polyadenylation are associated with cancer cell transformation, proliferation, and outcome. Researchers have developed methods to detect and analyze alternative polyadenylation as potential cancer biomarkers, which, if integrated into standard prognostic measures, may advance cancer prognostic testing and guide therapy. This review focuses on existing methodologies, both experimental and computational, to support the use of alternative polyadenylation as cancer biomarkers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Krzysztof J. Szkop, David S. Moss, Irene Nobeli
Summary: The study introduces a new beta-regression-based method flexiMAP for discovering differential alternative polyadenylation events in RNA-seq data. Results show that flexiMAP exhibits a good balance between specificity and sensitivity, and allows modeling of multiple confounding variables, improving the results of RNA-seq data analysis.
Article
Multidisciplinary Sciences
Lieke Michielsen, Marcel J. T. Reinders, Ahmed Mahfouz
Summary: scHPL is a hierarchical progressive learning method that can learn cellular hierarchies from multiple datasets while preserving the original annotations.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen
Summary: DISCO is an integrated database of single-cell omics data, offering an integrated cell atlas and harmonized metadata that users can utilize for comprehensive single-cell data analysis and exploration.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Genetics & Heredity
Wenbin Ye, Qiwei Lian, Congting Ye, Xiaohui Wu
Summary: Alternative polyadenylation (APA) plays important roles in modulating mRNA stability, translation, and subcellular localization, and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity. In this article, we provide an exhaustive overview of computational approaches for predicting poly(A) sites (pAs) from DNA sequences, bulk RNA sequencing (RNA-seq) data, and single-cell RNA sequencing (scRNA-seq) data. We examine several representative tools and provide operable suggestions on assessing the reliability of pAs predicted by different tools. We also propose practical guidelines on choosing appropriate methods applicable to diverse scenarios and discuss the challenges and opportunities in improving pA prediction using new techniques.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Alexander Gerniers, Orian Bricard, Pierre Dupont
Summary: This study presents a data mining method, MicroCellClust, to identify small subpopulations of cells with highly specific expression profiles. Through controlled experiments, it is shown to achieve a high F-1 score in identifying rare subpopulations of human T cells, specific CD4 T cells from breast cancer samples, and a subpopulation related to a specific stage in the cell cycle. Additionally, three rare subpopulations in mouse embryonic stem cells are successfully identified with MicroCellClust, demonstrating its effectiveness in identifying small subsets of cells with highly specific expression profiles.
Article
Biochemical Research Methods
Jordan W. Squair, Michael A. Skinnider, Matthieu Gautier, Leonard J. Foster, Gregoire Courtine
Summary: This study introduces a method called Augur for prioritizing the cell types most responsive to an experimental perturbation in complex tissue. By analyzing single-cell RNA-seq data, a list of cell types ranked based on separability following perturbation can be obtained. The study also demonstrates the application of this method in various workflows, including experimental designs, prioritization, and single-cell transcriptome imaging data.
Article
Biochemical Research Methods
Wenbin Ye, Tao Liu, Hongjuan Fu, Congting Ye, Guoli Ji, Xiaohui Wu
Summary: movAPA is an R package for modeling and visualizing alternative polyadenylation dynamics across different biological samples, providing functions for preprocessing, annotation, and statistical analysis of poly(A) sites, as well as identification of poly(A) signals, profiling of APA dynamics, and visualization. It offers seven metrics for measuring tissue-specificity or usages of APA sites across samples, and uses three methods for identifying 3' UTR shortening/lengthening events. It also allows exploration of APA site switching involving non-3' UTR polyadenylation.
Article
Plant Sciences
Yuze Zhao, Yifan Zhong, Congting Ye, Pingping Liang, Xiaobao Pan, Yuan-Ye Zhang, Yihui Zhang, Yingjia Shen
Summary: Our study revealed morphological differences and genetic differentiation among different populations of Kandelia obovata. The central population with abundant genetic diversity and high phenotypic plasticity had a wide plantable range but experienced reduced biomass after being transferred to other latitudes. Suppressed expression of lignin biosynthesis genes revealed by RNA-seq may be responsible for the biomass reduction. Additionally, modification of DNA methylation in MADS-box genes involved in the regulation of flowering time was observed, contributing to the adaptation to new environments.
Article
Biochemical Research Methods
Congting Ye, Danhui Zhao, Wenbin Ye, Xiaohui Wu, Guoli Ji, Qingshun Q. Li, Juncheng Lin
Summary: Alternative polyadenylation, the dynamic choice of different polyadenylation sites in a gene, plays important roles in various biological processes. The QuantifyPoly(A) method accurately quantifies genome-wide polyadenylation choices and reshapes polyadenylation profiles into novel clusters, revealing dynamic usage across biological samples and species specificity.
BRIEFINGS IN BIOINFORMATICS
(2021)
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.
Article
Genetics & Heredity
Lei Li, Linda Yu-Ling Lan, Lei Huang, Congting Ye, Jorge Andrade, Patrick C. C. Wilson
Summary: The Cookie toolkit efficiently selects representative samples from massive single-cell populations by quantifying relationships/similarities among samples and clustering them, showing higher efficacy and flexibility compared to conventional sampling methods.
FRONTIERS IN GENETICS
(2022)
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
Xiaoxuan Zhou, Yulin Weng, Wenyue Su, Congting Ye, Haidong Qu, Qingshun Quinn Li
Summary: In this study, the transcriptomic approach was used to investigate the development and germination processes of viviparous embryos in the mangrove species Kandelia obovata. Many key biological pathways and functional genes were found to play important roles in vivipary, including the reduction of abscisic acid and the precocious expression of genes involved in other phytohormones. These findings provide insight into the relationship between seed development and germination, and explain the combinatorial result of precocious loss of dormancy and enhanced germination potential during viviparous seed development.
FRONTIERS 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)
Review
Genetics & Heredity
Wenbin Ye, Qiwei Lian, Congting Ye, Xiaohui Wu
Summary: Alternative polyadenylation (APA) plays important roles in modulating mRNA stability, translation, and subcellular localization, and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity. In this article, we provide an exhaustive overview of computational approaches for predicting poly(A) sites (pAs) from DNA sequences, bulk RNA sequencing (RNA-seq) data, and single-cell RNA sequencing (scRNA-seq) data. We examine several representative tools and provide operable suggestions on assessing the reliability of pAs predicted by different tools. We also propose practical guidelines on choosing appropriate methods applicable to diverse scenarios and discuss the challenges and opportunities in improving pA prediction using new techniques.
GENOMICS PROTEOMICS & BIOINFORMATICS
(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
Biochemical Research Methods
Xiaohui Wu, Tao Liu, Congting Ye, Wenbin Ye, Guoli Ji
Summary: APA plays a crucial role in transcriptome diversity and gene expression regulation. The newly developed tool scAPAtrap can accurately identify poly(A) sites at the whole genome level in individual cells, even for sites with low read coverage, without relying on priori genome annotation. Compared to existing methods, scAPAtrap shows higher accuracy and sensitivity in identifying poly(A) sites, making it a valuable tool for exploring APA dynamics and heterogeneous APA isoform expression at the single-cell level.
BRIEFINGS IN BIOINFORMATICS
(2021)
