The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
U2AF1 mutations alter splice site recognition in hematological malignancies
Open accessAbstract
Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3′ splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find that U2AF1 mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure. U2AF1 mutations cause differential splicing of hundreds of genes, affecting biological pathways such as DNA methylation ( DNMT3B ), X chromosome inactivation ( H2AFY ), the DNA damage response ( ATR , FANCA ), and apoptosis ( CASP8 ). We show that U2AF1 mutations alter the preferred 3′ splice site motif in patients, in cell culture, and in vitro. Mutations affecting the first and second zinc fingers give rise to different alterations in splice site preference and largely distinct downstream splicing programs. These allele-specific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest that U2AF1 mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight into the normal function of U2AF1’s zinc finger domains.
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
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
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
Gene ontology analysis for RNA-seq: accounting for selection bias
Young, M. D., Wakefield, M. J., Smyth, G. K., & Oshlack, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-2-r14 · Cited by 7,107
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
The Cancer Genome Atlas Research Network (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1301689 · Cited by 5,078
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 · cited 1×
“Conservation is phastCons (Siepel et al. 2005) track from UCSC (Meyer et al.”
Frequent pathway mutations of splicing machinery in myelodysplasia
Yoshida, K., Sanada, M., Shiraishi, Y., Nowak, D., Nagata, Y., Yamamoto, R., Sato, Y., Sato-Otsubo, A., Kon, A., Nagasaki, M., et al. (2011) · Nature · doi:10.1038/nature10496 · Cited by 2,029
DNMT3A Mutations in Acute Myeloid Leukemia
Ley, T. J., Ding, L., Walter, M. J., McLellan, M. D., Lamprecht, T., Larson, D. E., Kandoth, C., Payton, J. E., Baty, J., Welch, J., et al. (2010) · New England Journal of Medicine · doi:10.1056/nejmoa1005143 · Cited by 1,983
Leaver-Fay (2011) · doi:10.1016/b978-0-12-381270-4.00019-6 · Cited by 1,904
Somatic SF3B1 Mutation in Myelodysplasia with Ring Sideroblasts
Papaemmanuil, E., Cazzola, M., Boultwood, J., Malcovati, L., Vyas, P., Bowen, D., Pellagatti, A., Wainscoat, J. S., Hellstrom-Lindberg, E., Gambacorti-Passerini, C., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1103283 · Cited by 1,222
Cited by
U1 snRNP regulates cancer cell migration and invasion in vitro
Oh, J.-M., Venters, C. C., Di, C., Pinto, A. M., Wan, L., Younis, I., Cai, Z., Arai, C., So, B. R., Duan, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13993-7 · Cited by 7,157
RNA splicing dysregulation and the hallmarks of cancer
Bradley, R. K., & Anczuków, O. (2023) · Nature Reviews Cancer · doi:10.1038/s41568-022-00541-7 · Cited by 579
Self-citationSRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition
Kim, E., Ilagan, J. O., Liang, Y., Daubner, G. M., Lee, S. C.-W., Ramakrishnan, A., Li, Y., Chung, Y. R., Micol, J.-B., Murphy, M. E., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.04.006 · Cited by 575
Self-citationMutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo
Shirai, C. L., Ley, J. N., White, B. S., Kim, S., Tibbitts, J., Shao, J., Ndonwi, M., Wadugu, B., Duncavage, E. J., Okeyo-Owuor, T., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.04.008 · Cited by 287
Predicting RNA splicing from DNA sequence using Pangolin
Zeng, T., & Li, Y. I. (2022) · Genome Biology · doi:10.1186/s13059-022-02664-4 · Cited by 283
Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations
Lee, S. C.-W., North, K., Kim, E., Jang, E., Obeng, E., Lu, S. X., Liu, B., Inoue, D., Yoshimi, A., Ki, M., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.07.003 · Cited by 219
Self-citationMinor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition
Inoue, D., Polaski, J. T., Taylor, J., Castel, P., Chen, S., Kobayashi, S., Hogg, S. J., Hayashi, Y., Pineda, J. M. B., El Marabti, E., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00828-9 · Cited by 108
Self-citationAberrant splicing and drug resistance in AML
de Necochea-Campion, R., Shouse, G. P., Zhou, Q., Mirshahidi, S., & Chen, C.-S. (2016) · Journal of Hematology & Oncology · doi:10.1186/s13045-016-0315-9 · Cited by 66
Metadata
- Authors
- Ilagan, J. O., Ramakrishnan, A., Hayes, B., Murphy, M. E., Zebari, A. S., Bradley, P., & Bradley, R. K.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2014-09-29
- Volume
- 25
- Issue
- 1
- Pages
- 14-26
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2131769243
- Cited by
- 287
- References
- 9
- Type
- posted content
- Language
- en
- Open access
- bronze
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.
