The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers
Open accessAbstract
Mutations in the splicing factor SF3B1 are found in several cancer types and have been associated with various splicing defects. Using transcriptome sequencing data from chronic lymphocytic leukemia, breast cancer and uveal melanoma tumor samples, we show that hundreds of cryptic 3' splice sites (3'SSs) are used in cancers with SF3B1 mutations. We define the necessary sequence context for the observed cryptic 3' SSs and propose that cryptic 3'SS selection is a result of SF3B1 mutations causing a shift in the sterically protected region downstream of the branch point. While most cryptic 3'SSs are present at low frequency (<10%) relative to nearby canonical 3'SSs, we identified ten genes that preferred out-of-frame cryptic 3'SSs. We show that cancers with mutations in the SF3B1 HEAT 5-9 repeats use cryptic 3'SSs downstream of the branch point and provide both a mechanistic model consistent with published experimental data and affected targets that will guide further research into the oncogenic effects of SF3B1 mutation.
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Cutadapt removes adapter sequences from high-throughput sequencing reads
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Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes
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Frequent pathway mutations of splicing machinery in myelodysplasia
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Somatic SF3B1 Mutation in Myelodysplasia with Ring Sideroblasts
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Ule, J., & Blencowe, B. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.017 · Cited by 780
Therapeutic targeting of splicing in cancer
Lee, S. C.-W., & Abdel-Wahab, O. (2016) · Nature Medicine · doi:10.1038/nm.4165 · Cited by 561
Obeng, E. A., Chappell, R. J., Seiler, M., Chen, M. C., Campagna, D. R., Schmidt, P. J., Schneider, R. K., Lord, A. M., Wang, L., Gambe, R. G., et al. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.08.006 · Cited by 380
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
Mutations in the RNA Splicing Factor SF3B1 Promote Tumorigenesis through MYC Stabilization
Liu, Z., Yoshimi, A., Wang, J., Cho, H., Chun-Wei Lee, S., Ki, M., Bitner, L., Chu, T., Shah, H., Liu, B., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-1330 · Cited by 118
Metadata
- Authors
- DeBoever, C., Ghia, E. M., Shepard, P. J., Rassenti, L., Barrett, C. L., Jepsen, K., Jamieson, C. H. M., Carson, D., Kipps, T. J., & Frazer, K. A.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-03-13
- Volume
- 11
- Issue
- 3
- Pages
- e1004105
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2030364523
- Cited by
- 211
- References
- 9
- FWCI
- 10.04
- Type
- journal article
- Language
- en
- Open access
- gold
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- DeBoever, C., Ghia, E. M., Shepard, P. J., Rassenti, L., Barrett, C. L., Jepsen, K., Jamieson, C. H. M., Carson, D., Kipps, T. J., & Frazer, K. A. (2015). Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1004105
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