ArticleNucleic acids research2008
Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed, 173 citations in OpenAlex.
- A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails.Genome biology · 2026Article
- Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability.Nature communications · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
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- Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (International journal of molecular sciences · 2023Article
- A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis.G3 (Bethesda, Md.) · 2023Article
- stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies.Genomics, proteomics & bioinformatics · 2023Article
- Plant terminators: the unsung heroes of gene expression.Journal of experimental botany · 2023Review
- Alternative Polyadenylation Is a Novel Strategy for the Regulation of Gene Expression in Response to Stresses in Plants.International journal of molecular sciences · 2023Review
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Genome-wide alternative polyadenylation dynamics underlying plant growth retardant-induced dwarfing of pomegranate.Frontiers in plant science · 2023Article
- Plant Promoters and Terminators for High-Precision Bioengineering.Biodesign research · 2023Review
- Article
- An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development.Genome biology · 2022Article
- Analysis Polyadenylation Signal Usage inAnimals : an open access journal from MDPI · 2022Article
- Signatures of mRNA Alternative Polyadenylation inFrontiers in genetics · 2022Article
- Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa.BMC genomics · 2021Article
- Expression Elements Derived From Plant Sequences Provide Effective Gene Expression Regulation and New Opportunities for Plant Biotechnology Traits.Frontiers in plant science · 2021Article
- Use of synthetic biology tools to optimize the production of active nitrogenase Fe protein in chloroplasts of tobacco leaf cells.Plant biotechnology journal · 2020Article
- Transcription Terminator-Mediated Enhancement in Transgene Expression in Maize: Preponderance of the AUGAAU Motif Overlapping With Poly(A) Signals.Frontiers in plant science · 2020Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3'-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5'-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites.
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