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.
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Cites
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
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Gene ontology analysis for RNA-seq: accounting for selection bias
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“Conservation is phastCons (Siepel et al. 2005) track from UCSC (Meyer et al.”
Frequent pathway mutations of splicing machinery in myelodysplasia
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DNMT3A Mutations in Acute Myeloid Leukemia
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Somatic SF3B1 Mutation in Myelodysplasia with Ring Sideroblasts
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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
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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
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- Ilagan, J. O., Ramakrishnan, A., Hayes, B., Murphy, M. E., Zebari, A. S., Bradley, P., & Bradley, R. K. (2015). U2AF1 mutations alter splice site recognition in hematological malignancies. Genome Research. https://doi.org/10.1101/gr.181016.114
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