The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing
Open accessAbstract
Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3′ region extraction and deep sequencing (3′READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. Thorough annotation of gene 3′ ends revealed over 5,000 previously overlooked pAs (∼8% of total) flanked by A-rich sequences, underscoring the necessity of using an accurate tool for pA mapping. About 79% of mRNA genes and 66% of long noncoding RNA genes undergo APA, but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Quantitative analysis of APA isoforms by 3′READS indicated that promoter-distal pAs, regardless of intron or exon locations, become more abundant during embryonic development and cell differentiation and that upregulated isoforms have stronger pAs, suggesting global modulation of the 3′ end–processing activity in development and differentiation.
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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Alternative isoform regulation in human tissue transcriptomes
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
Mayr, C., & Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.06.016 · Cited by 1,613
Mechanism and regulation of mRNA polyadenylation
Colgan, D. F., & Manley, J. L. (1997) · Genes & Development · doi:10.1101/gad.11.21.2755 · Cited by 784
Mechanisms and Consequences of Alternative Polyadenylation
Di Giammartino, D. C., Nishida, K., & Manley, J. L. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.017 · Cited by 737
Flavell, S. W., Kim, T.-K., Gray, J. M., Harmin, D. A., Hemberg, M., Hong, E. J., Markenscoff-Papadimitriou, E., Bear, D. M., & Greenberg, M. E. (2008) · Neuron · doi:10.1016/j.neuron.2008.11.029 · Cited by 440
Ji, Z., & Tian, B. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008419 · Cited by 264
Self-citation
Cited by
Alternative polyadenylation of mRNA precursors
Tian, B., & Manley, J. L. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.116 · Cited by 1,179
Self-citationMayr, C. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a034728 · Cited by 519
TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications
Chang, H., Lim, J., Ha, M., & Kim, V. N. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.007 · Cited by 454
Alternative mRNA transcription, processing, and translation: insights from RNA sequencing
de Klerk, E., & ‘t Hoen, P. A. C. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.01.001 · Cited by 350
Context-specific regulation and function of mRNA alternative polyadenylation
Mitschka, S., & Mayr, C. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00507-5 · Cited by 336
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
Self-citationNishimoto, Y., Nakagawa, S., Hirose, T., Okano, H., Takao, M., Shibata, S., Suyama, S., Kuwako, K.-I., Imai, T., Murayama, S., et al. (2013) · Molecular Brain · doi:10.1186/1756-6606-6-31 · Cited by 272
Wang, R., Nambiar, R., Zheng, D., & Tian, B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1000 · Cited by 239
Self-citationRNA polymerase II speed: a key player in controlling and adapting transcriptome composition
Muniz, L., Nicolas, E., & Trouche, D. (2021) · The EMBO Journal · doi:10.15252/embj.2020105740 · Cited by 198
“Alternative polyadenylation is very common in eukaryotes, and around 70% of mammalian protein-coding genes are subjected to alternative polyadenylation (Derti et al , 2012; Hoque et al , 2013).”
PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing
Herrmann, C. J., Schmidt, R., Kanitz, A., Artimo, P., Gruber, A. J., & Zavolan, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz918 · Cited by 196
van den Hoogenhof (2016) · doi:10.1161/circresaha.115.307872 · Cited by 134
Yang, S. W., Li, L., Connelly, J. P., Porter, S. N., Kodali, K., Gan, H., Park, J. M., Tacer, K. F., Tillman, H., Peng, J., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.022 · Cited by 79
Self-citationHwang, H.-W., Saito, Y., Park, C. Y., Blachère, N. E., Tajima, Y., Fak, J. J., Zucker-Scharff, I., & Darnell, R. B. (2017) · Neuron · doi:10.1016/j.neuron.2017.08.024 · Cited by 74
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
Self-citationDeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning
Li, Z., Li, Y., Zhang, B., Li, Y., Long, Y., Zhou, J., Zou, X., Zhang, M., Hu, Y., Chen, W., et al. (2022) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.05.004 · Cited by 37
Metadata
- Authors
- Hoque, M., Ji, Z., Zheng, D., Luo, W., Li, W., You, B., Park, J. Y., Yehia, G., & Tian, B.
- Venue
- Nature Methods
- Published
- 2012-12-16
- Volume
- 10
- Issue
- 2
- Pages
- 133-139
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2108264419
- Cited by
- 440
- References
- 9
- FWCI
- 8.71
- 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
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.
