Cited by 196RNA Research and SplicingGenomics and Phylogenetic StudiesRNA regulation and disease

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PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing

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Herrmann, Christina J, Schmidt, Ralf, Kanitz, Alexander, Artimo, Panu, Gruber, Andreas J, Zavolan, Mihaela·2019·Nucleic Acids Research

DOI 10.1093/nar/gkz918PMC PMC7145510

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Abstract

Generated by 3' end cleavage and polyadenylation at alternative polyadenylation (poly(A)) sites, alternative terminal exons account for much of the variation between human transcript isoforms. More than a dozen protocols have been developed so far for capturing and sequencing RNA 3' ends from a variety of cell types and species. In previous studies, we have used these data to uncover novel regulatory signals and cell type-specific isoforms. Here we present an update of the PolyASite (https://polyasite.unibas.ch) resource of poly(A) sites, constructed from publicly available human, mouse and worm 3' end sequencing datasets by enforcing uniform quality measures, including the flagging of putative internal priming sites. Through integrated processing of all data, we identified and clustered sites that are closely spaced and share polyadenylation signals, as these are likely the result of stochastic variations in processing. For each cluster, we identified the representative - most frequently processed - site and estimated the relative use in the transcriptome across all samples. We have established a modern web portal for efficient finding, exploration and export of data. Database generation is fully automated, greatly facilitating incorporation of new datasets and the updating of underlying genome resources.

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FAIRsharing record for: PolyASite
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Self-citation

Authors: Herrmann, C. J., Schmidt, R., Kanitz, A., Artimo, P., Gruber, A. J., & Zavolan, M.
Affiliations: University of Basel (CH)
SIB Swiss Institute of Bioinformatics (CH)
University of Oxford (GB)
Corresponding author: Zavolan, Mihaela
ORCID: Herrmann, Christina J
Schmidt, Ralf
Kanitz, Alexander
Gruber, Andreas J
Zavolan, Mihaela
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2019-10-16
Volume: 48
Issue: D1
Pages: D174-D179
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkz918
PMC: PMC7145510
OpenAlex: W2980708325
Cited by: 196
References: 32
Citations by year: 2026: 18 · 2025: 21 · 2024: 33 · 2023: 36 · 2022: 37 · 2021: 40 · 2020: 10 · 2019: 1
FWCI: 7.28
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/4.0/ (vor)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
KOPS (University of Konstanz) (submittedVersion, cc-by-nc)
edoc (University of Basel) (submittedVersion)
Funders: Swiss National Science Foundation (31003A_170216, 51NF40_141735)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords: polyadenylation sites, alternative polyadenylation, 3' end sequencing, mRNA isoforms, site clustering, web portal
MeSH terms: Animals, Humans, Poly A, Caenorhabditis elegans, Sequence Analysis, RNA, Polyadenylation, Databases, Nucleic Acid, Mice

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PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing

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