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Updated: Jan 17, 2026
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution
Pei-Hong Zhang1,2, Hua Feng1, Xu-Kai Ma1
1Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
This study profiles polyadenylation site (PAS) usage across seven species using the SCAPTURE v2 tool on scRNA-seq data. It reveals species-specific PAS preferences and introduces PASSpedia, a comprehensive database for PAS analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Polyadenylation site (PAS) selection is crucial for gene expression regulation.
- Alternative polyadenylation (APA) isoform expression is studied using 3' tag sequencing in RNA-seq data.
- Previous methods for PAS analysis in single-cell RNA sequencing (scRNA-seq) have limitations.
Purpose of the Study:
- To upgrade the SCAPTURE pipeline (v2) for comprehensive PAS profiling.
- To analyze PAS usage across seven species using a large scRNA-seq dataset.
- To create a publicly accessible database (PASSpedia) for cross-species PAS comparison.
Main Methods:
- Applied the deep learning-based SCAPTURE v2 pipeline to 1330 3' tag-based scRNA-seq datasets.
- Validated SCAPTURE's single-cell PAS profiling accuracy using long-read sequencing data.
- Compared PAS usage patterns across different species, including human and mouse.
Main Results:
- Generated a comprehensive PAS landscape across seven species at single-cell resolution.
- Demonstrated high accuracy of SCAPTURE v2, identifying novel PASs.
- Identified distinct, species-specific PAS usage preferences, independent of gene expression conservation.
Conclusions:
- SCAPTURE v2 accurately profiles single-cell PAS usage across diverse species.
- PASSpedia provides a valuable resource for comparative PAS analysis.
- Species-specific APA contributes to biological diversity beyond conserved gene expression.
