ArticleProceedings of the National Academy of Sciences of the United States of America2011
Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers.
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Who cites it
172 citing papers in PubMed, 309 citations in OpenAlex.
- Identification of specific transcripts for plant heat stress tolerance through genome-wide analysis of SIZ1-dependent alternative polyadenylation.Stress biology · 2026Article
- Alternative Polyadenylation Dynamics During the Rice Blast Immune Response.Molecular plant pathology · 2026Article
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- Exploiting plant immune "switches" for resistance engineering.Stress biology · 2026Review
- A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails.Genome biology · 2026Article
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Polyadenylation Complex CFII Recognizes Downstream Cis-element for Pre-mRNA Polyadenylation Through Interaction with an RNA-Binding Protein in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- RNA-binding proteins orchestrating immunity in plants.The Plant journal : for cell and molecular biology · 2025Review
- A cis-natural antisense RNA regulates alternative polyadenylation of SlSPX5 under Pi starvation in tomato.Nature communications · 2025Article
- Alternative polyadenylation and metabolic profiling in young panicle development of hybrid rice and its parents.Rice (New York, N.Y.) · 2025Article
- Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination.Nature communications · 2025Article
- Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogenbioRxiv : the preprint server for biology · 2025Article
- Review
- Article
- Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA.Briefings in bioinformatics · 2024Article
- The Arabidopsis U1 snRNP regulates mRNA 3'-end processing.Nature plants · 2024Article
- Source leaves are regulated by sink strengths through non-coding RNAs and alternative polyadenylation in cucumber (Cucumis sativus L.).BMC plant biology · 2024Article
- Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability.Nature communications · 2024Article
- Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut.Plant biotechnology journal · 2024Article
112 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3'UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of Arabidopsis genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.