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PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing
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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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“To reduce the risk of picking genes in which the perceived APA is driven by 3′ bias in the GTEx RNA-seq data, we required that the genes also exhibited differential distal polyadenylation in cell-type-matched experiments from the PolyASite 2.0 database42.”
From Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation (2025) · cites this paper as [42]
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“For example, RWDD1 exhibits biased usage of the distal-most PAS in brain42 (Fig. 2e; see Extended Data Fig. 3b for additional examples).”
From Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation (2025) · cites this paper as [42]
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Cites
Leinonen, R., Sugawara, H., & Shumway, M. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1019 · Cited by 2,872
Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A., & Burge, C. B. (2008) · Science · doi:10.1126/science.1155390 · Cited by 1,349
A large-scale analysis of mRNA polyadenylation of human and mouse genes
Tian, B. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki158 · Cited by 970
Cunningham, F., Achuthan, P., Akanni, W., Allen, J., Amode, M. R., Armean, I. M., Bennett, R., Bhai, J., Billis, K., Boddu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1113 · Cited by 925
The UCSC Genome Browser database: 2019 update
Haeussler, M., Zweig, A. S., Tyner, C., Speir, M. L., Rosenbloom, K. R., Raney, B. J., Lee, C. M., Lee, B. T., Hinrichs, A. S., Gonzalez, J. N., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1095 · Cited by 879
Patterns of Variant Polyadenylation Signal Usage in Human GenesPreprint
Beaudoing, E., Freier, S. M., Wyatt, J. R., Claverie, J., & Gautheret, D. (2000) · Genome Research · doi:10.1101/gr.10.7.1001 · Cited by 676
A quantitative atlas of polyadenylation in five mammalsPreprint
Derti, A., Garrett-Engele, P. W., MacIsaac, K. D., Stevens, R. C., Sriram, S., Chen, R., Rohl, C. A., Johnson, J. M., & Babak, T. (2012) · Genome Research · doi:10.1101/gr.132563.111 · Cited by 663
Ji, Z., Lee, J. Y., Pan, Z., Jiang, B., & Tian, B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900028106 · Cited by 609
Edmonds, M., Vaughan, M. H., & Nakazato, H. (1971) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.68.6.1336 · Cited by 510
Alternative cleavage and polyadenylation in health and disease
Gruber, A. J., & Zavolan, M. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0145-z · Cited by 493
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Pardo-Palacios, F. J., Arzalluz-Luque, Á., Kondratova, L., Salguero, P., Mestre‐Tomás, J., Amorín, R., Estevan-Morió, E., Liu, T., Nanni, A. V., McIntyre, L. M., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02229-2 · Cited by 219
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Dondi, A., Lischetti, U., Jacob, F., Singer, F., Borgsmüller, N., Coelho, R., Aebersold, R. H., Ak, M., Alquaddoomi, F., Albert, S. I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43387-9 · Cited by 55
Wu, X., Liu, T., Ye, C., Ye, W., & Ji, G. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa273 · Cited by 53
Yamaguchi, K., Ishigaki, K., Suzuki, A., Tsuchida, Y., Tsuchiya, H., Sumitomo, S., Nagafuchi, Y., Miya, F., Tsunoda, T., Shoda, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32358-1 · Cited by 51
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Stroup, E. K., & Ji, Z. (2023) · Nature Communications · doi:10.1038/s41467-023-43266-3 · Cited by 40
Yang, Y., Yang, R., Kang, B., Qian, S., He, X., & Zhang, X. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113335 · Cited by 41
Li, G., Fang, N., Yuan, G.-H., Liu, C., Liu, X., Chen, L., Tian, B., & Yang, L. C. (2021) · Genome biology · doi:10.1186/s13059-021-02437-5 · Cited by 40
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Zhao, Z., Xu, Q., Wei, R., Wang, W., Ding, D., Yang, Y., Yao, J., Zhang, L., Hu, Y., Wei, G., et al. (2021) · Genome Research · doi:10.1101/gr.271627.120 · Cited by 40
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Jin, W., Zhu, Q., Yang, Y., Yang, W., Wang, D., Yang, J., Niu, X., Yu, D., & Gong, J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa778 · Cited by 26
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Zhao, Z., Xu, Q., Wei, R., Huang, L., Wang, W., Wei, G., & Ni, T. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab772 · Cited by 27
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Ueda, M. T., Inamo, J., Miya, F., Shimada, M., Yamaguchi, K., & Kochi, Y. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100654 · Cited by 20
Bryce-Smith, S., Bürri, D., Gazzara, M. R., Herrmann, C., Danecka, W., Fitzsimmons, C. M., Wan, Y. K., Zhuang, F., Fansler, M. M., Fernández, J. M., et al. (2023) · RNA · doi:10.1261/rna.079849.123 · Cited by 18
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Rad, S. M. A. H., Halpin, J. C., Tawinwung, S., Suppipat, K., Hirankarn, N., & McLellan, A. D. (2022) · Immunology and Cell Biology · doi:10.1111/imcb.12551 · Cited by 18
Moon, Y., Herrmann, C., Mironov, A., & Zavolan, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1043 · Cited by 16
Self-citationGallardo, C. M., de Diego, A. S., Martínez‐A, C., & van Wely, K. H. M. (2021) · Transcription · doi:10.1080/21541264.2021.1959244 · Cited by 15
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van der Noord, V. E., van der Stel, W., Louwerens, G., Verhoeven, D., Kuiken, H. J., Lieftink, C., Grandits, M., Ecker, G. F., Beijersbergen, R. L., Bouwman, P., et al. (2023) · Breast Cancer Research · doi:10.1186/s13058-023-01648-x · Cited by 15
Li, N., Cai, Y., Zou, M., Zhou, J. P., Zhang, L., Zhou, L., Xiang, W., Cui, Y., & Li, H. (2022) · Stem Cell Reports · doi:10.1016/j.stemcr.2022.11.016 · Cited by 14
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Long, Y., Zhang, B., Tian, S., Chan, J. J., Zhou, J., Li, Z., Li, Y., An, Z., Liao, X., Wang, Y., et al. (2023) · Genome Research · doi:10.1101/gr.277177.122 · Cited by 12
Kang, B., Yang, Y., Hu, K., Ruan, X., Liu, Y.-L., Lee, P., Lee, J., Wang, J., & Zhang, X. (2023) · Genome Research · doi:10.1101/gr.277864.123 · Cited by 11
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Jonnakuti, V. S., Wagner, E. J., Maletić‐Savatić, M., Liu, Z., & Yalamanchili, H. K. (2024) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100707 · Cited by 9
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Fahmi, N. A., Saha, S., Song, Q., Lou, Q., Yong, J., & Zhang, W. (2025) · Experimental & Molecular Medicine · doi:10.1038/s12276-025-01496-z · Cited by 10
Liu, X., Chen, H., Li, Z., Yang, X., Jin, W., Wang, Y., Zheng, J., Li, L., Xuan, C., Yuan, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46875-8 · Cited by 9
Kandhari, N., Kraupner-Taylor, C. A., Harrison, P. F., Powell, D., & Beilharz, T. H. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22105322 · Cited by 11
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Hsu, J., Jarroux, J., Joglekar, A., Romero, J. P., Nemec, C. M., Reyes, D., Royall, A., He, Y., Belchikov, N., Leo, K. T., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.27.514084 · Cited by 13
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Sahrhage, M., Paul, N. B., Beißbarth, T., & Haubrock, M. (2024) · Life Science Alliance · doi:10.26508/lsa.202302380 · Cited by 10
Pritts, J. D., Oluyadi, A. A., Huang, W., Shimberg, G. D., Kane, M. A., Wilks, A., & Michel, S. L. J. (2021) · Biochemistry · doi:10.1021/acs.biochem.0c00940 · Cited by 9
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Xu, S.-M., Curry‐Hyde, A., Sytnyk, V., & Janitz, M. (2022) · Gene · doi:10.1016/j.gene.2021.146133 · Cited by 9
Ji, G., Tang, Q., Zhu, S. Z., Zhu, J., Ye, P., Xia, S., & Wu, X. (2023) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2023.01.003 · Cited by 8
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Pruunsild, P., Bengtson, C. P., Loss, I., Lohrer, B., & Bading, H. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104671 · Cited by 8
Melo, A. R. V., Raposo, M., Ventura, M., Martins, S., Pavão, S., Alonso, I. D. C. M. P., Bettencourt, C., & Lima, M. C. F. (2022) · The Cerebellum · doi:10.1007/s12311-021-01358-0 · Cited by 8
Salmén, F., Jonghe, J. D., Kamiński, T. S., Alemany, A., Parada, G. E., Verity-Legg, J., Yanagida, A., Kohler, T. N., Battich, N., van den Brekel, F., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.15.460240 · Cited by 8
Pandini, C., Pagani, G., Tassinari, M., Vitale, E., Bezzecchi, E., Saadeldin, M. K., Doldi, V., Giannuzzi, G., Mantovani, R., Chiara, M., et al. (2024) · Cell Death and Disease · doi:10.1038/s41419-024-06576-y · Cited by 7
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Okumura, K., Saito, M., Isogai, E., Tokunaga, Y., Hasegawa, Y., Araki, K., & Wakabayashi, Y. (2022) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2022.02.009 · Cited by 7
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Metadata
- 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
- 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
- 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
- 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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