ArticleBMC genomics2003
Sequence determinants in human polyadenylation site selection.
Article in BMC genomics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed, 169 citations in OpenAlex.
- A conserved 3'UTR short motif regulates gene expression in vertebrates.Nucleic acids research · 2026Article
- PolyA-GLM: A comprehensive framework forComputational and structural biotechnology journal · 2026Article
- The Dynamic Landscape of 3'-UTR Alternative Polyadenylation Across Mouse Fetal Development and Anatomy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS.NAR genomics and bioinformatics · 2023Article
- Known sequence features explain half of all human gene ends.NAR genomics and bioinformatics · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Complex Transcriptional Profiles of theCells · 2022Article
- Precise gene models using long-read sequencing reveal a unique poly(A) signal inRNA (New York, N.Y.) · 2022Article
- From shallow to deep: some lessons learned from application of machine learning for recognition of functional genomic elements in human genome.Human genomics · 2022Review
- Alternative polyadenylation by sequential activation of distal and proximal PolyA sites.Nature structural & molecular biology · 2022Article
- Dynamic Variations of 3'UTR Length Reprogram the mRNA Regulatory Landscape.Biomedicines · 2021Review
- MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome.Non-coding RNA · 2021Article
- Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.Nature communications · 2021Article
- In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.Genome biology · 2021Article
- Alternative Polyadenylation: a new frontier in post transcriptional regulation.Biomarker research · 2020Review
- Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species.PLoS computational biology · 2020Article
- Sequence determinants of polyadenylation-mediated regulation.Genome research · 2019Article
- Cell Cycle Kinase Polo Is Controlled by a Widespread 3' Untranslated Region Regulatory Sequence in Drosophila melanogaster.Molecular and cellular biology · 2019Article
- Modeling of Genome-Wide Polyadenylation Signals inFrontiers in genetics · 2019Article
- Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus.BMC genomics · 2018Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDifferential polyadenylation is a widespread mechanism in higher eukaryotes producing mRNAs with different 3' ends in different contexts. This involves several alternative polyadenylation sites in the 3' UTR, each with its specific strength. Here, we analyze the vicinity of human polyadenylation signals in search of patterns that would help discriminate strong and weak polyadenylation sites, or true sites from randomly occurring signals.
resultsWe used human genomic sequences to retrieve the region downstream of polyadenylation signals, usually absent from cDNA or mRNA databases. Analyzing 4956 EST-validated polyadenylation sites and their -300/+300 nt flanking regions, we clearly visualized the upstream (USE) and downstream (DSE) sequence elements, both characterized by U-rich (not GU-rich) segments. The presence of a USE and a DSE is the main feature distinguishing true polyadenylation sites from randomly occurring A(A/U)UAAA hexamers. While USEs are indifferently associated with strong and weak poly(A) sites, DSEs are more conspicuous near strong poly(A) sites. We then used the region encompassing the hexamer and DSE as a training set for poly(A) site identification by the ERPIN program and achieved a prediction specificity of 69 to 85% for a sensitivity of 56%.
conclusionThe availability of complete genomes and large EST sequence databases now permit large-scale observation of polyadenylation sites. Both U-rich sequences flanking both sides of poly(A) signals contribute to the definition of "true" sites. However, the downstream U-rich sequences may also play an enhancing role. Based on this information, poly(A) site prediction accuracy was moderately but consistently improved compared to the best previously available algorithm.
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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.