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Updated: May 30, 2026
08:35
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants
Yingjia Shen1, R C Venu, Kan Nobuta
1Department of Botany, Miami University, Oxford, OH 45056, USA
Genome Research
|August 5, 2011
Summary
Alternative polyadenylation (APA) significantly impacts gene expression and transcriptome diversity in plants. This study reveals widespread APA usage in Arabidopsis and rice, influencing gene regulation across development and environmental responses.
Area of Science:
- Molecular Biology
- Genomics
- Plant Science
Background:
- Alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism.
- APA influences mRNA sequence elements, coding capacity, gene expression, and transcriptome diversity.
- Understanding APA's role in transcriptome dynamics is crucial for plant biology.
Purpose of the Study:
- To investigate the prevalence and dynamics of APA in plants.
- To analyze the contribution of APA to transcriptome diversity across various conditions.
- To identify conserved APA events between rice and Arabidopsis.
Main Methods:
- Analysis of large-scale RNA tag data from digital gene expression (DGE) protocols.
- Utilized massively parallel signature sequencing (MPSS-DGE) and Illumina sequencing-by-synthesis (SBS-DGE) platforms.
- Examined data from diverse tissues, developmental stages, and experimental treatments (mutations, environmental exposures).
Main Results:
- Approximately 60% of Arabidopsis genes and 47%-82% of rice genes exhibit APA.
- A significant proportion of APA events (49%-66%) occur upstream of annotated stop codons.
- APA transcripts constitute about 10% of the transcriptome and show differential distribution during development and stress responses.
- Conserved APA events were identified in 3034 genes between rice and Arabidopsis.
Conclusions:
- APA is a widespread and dynamic regulatory mechanism in plants, contributing significantly to transcriptome diversity.
- APA plays a role in developmental and environmental responses, offering an additional layer of gene regulation.
- Conserved APA events highlight fundamental roles in plant gene regulation across species.
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01:10Transcription
Overview
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