The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation
Open accessAbstract
Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3′UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of Arabidopsis genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Mayr, C., & Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.06.016 · Cited by 1,613
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
Swarbreck, D., Wilks, C., Lamesch, P., Berardini, T. Z., Garcia-Hernandez, M., Foerster, H., Li, D., Meyer, T., Muller, R., Ploetz, L., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm965 · Cited by 1,074
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 956
Bidirectional promoters generate pervasive transcription in yeast
Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Münster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W., & Steinmetz, L. M. (2009) · Nature · doi:10.1038/nature07728 · Cited by 926
Regulatory roles of natural antisense transcripts
Faghihi, M. A., & Wahlestedt, C. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2738 · Cited by 736
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
Neil, H., Malabat, C., d’Aubenton-Carafa, Y., Xu, Z., Steinmetz, L. M., & Jacquier, A. (2009) · Nature · doi:10.1038/nature07747 · Cited by 604
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 595
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function
Isken, O., & Maquat, L. E. (2007) · Genes & Development · doi:10.1101/gad.1566807 · Cited by 592
Exosome-Mediated Recognition and Degradation of mRNAs Lacking a Termination Codon
van Hoof, A., Frischmeyer, P. A., Dietz, H. C., & Parker, R. (2002) · Science · doi:10.1126/science.1067272 · Cited by 591
An mRNA Surveillance Mechanism That Eliminates Transcripts Lacking Termination Codons
Frischmeyer, P. A., van Hoof, A., O'Donnell, K., Guerrerio, A. L., Parker, R., & Dietz, H. C. (2002) · Science · doi:10.1126/science.1067338 · Cited by 590
Cited by
Alternative cleavage and polyadenylation: the long and short of it
Tian, B., & Manley, J. L. (2013) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2013.03.005 · Cited by 306
Alternative polyadenylation: New insights from global analyses
Shi, Y. (2012) · RNA · doi:10.1261/rna.035899.112 · Cited by 212
Liu, X., Freitas, J., Zheng, D., Oliveira, M. S., Hoque, M., Martins, T., Henriques, T., Tian, B., & Moreira, A. (2017) · RNA · doi:10.1261/rna.062661.117 · Cited by 67
Metadata
- Authors
- Wu, X., Liu, M., Downie, B., Liang, C., Ji, G., Li, Q. Q., & Hunt, A. G.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2011-07-11
- Volume
- 108
- Issue
- 30
- Pages
- 12533-12538
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2083196263
- Cited by
- 300
- References
- 44
- FWCI
- 8.35
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. https://app.cochat.ai/papers/10.1073/pnas.1019732108
- The paper
- Wu, X., Liu, M., Downie, B., Liang, C., Ji, G., Li, Q. Q., & Hunt, A. G. (2011). Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1019732108
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
