ArticlePlant physiology2005
Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures.
Article in Plant physiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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117 citing papers in PubMed.
- Identification of specific transcripts for plant heat stress tolerance through genome-wide analysis of SIZ1-dependent alternative polyadenylation.Stress biology · 2026Article
- Telomere-to-telomere genome assembly of Metarhizium acridum provides insights into Metarhizium genome evolution.BMC genomics · 2026Article
- MicroRNA-Induced Gene Silencing (MIGS): A Tool for Multi-Gene Silencing and Targeting Viruses in Plants.Plant biotechnology journal · 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
- Genomic language models with k-mer tokenization strategies for plant genome annotation and regulatory element strength prediction.Plant molecular biology · 2025Article
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- The Arabidopsis U1 snRNP regulates mRNA 3'-end processing.Nature plants · 2024Article
- The general transcription factors (GTFs) of RNA polymerase II and their roles in plant development and stress responses.Critical reviews in biochemistry and molecular biology · 2024Review
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability.Nature communications · 2024Article
- A foundational large language model for edible plant genomes.Communications biology · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- Article
- Dynamics of alternative polyadenylation in single root cells ofFrontiers in plant science · 2024Article
- Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation.Molecular horticulture · 2023Review
- The expanding role of RNA modifications in plant RNA polymerase II transcripts: highlights and perspectives.Journal of experimental botany · 2023Review
- A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis.G3 (Bethesda, Md.) · 2023Article
- Plant terminators: the unsung heroes of gene expression.Journal of experimental botany · 2023Review
57 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
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Abstract
Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3'-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3'-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3'-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3'-ends for gene annotation.
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