Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point

Darman, Rachel; Seiler, Michael; Agrawal, Anant A.; Lim, Kian Huat; Peng, Shouyong; Aird, Daniel; Bailey, Suzanna; Bhavsar, Erica B.; Chan, Betty; Colla, Simona; Corson, Laura; Feala, Jacob; Fekkes, Peter; Ichikawa, Kana; Keaney, Gregg F.; Lee, Linda; Kumar, Pavan; Kunii, Kaiko; MacKenzie, Crystal; Matijevic, Mark; Mizui, Yoshiharu; Myint, Khin Than; Park, Eun Sun; Puyang, Xiaoling; Selvaraj, Anand; Thomas, Michael; Tsai, Jennifer; Wang, John Y.; Warmuth, Markus; Yang, Hui; Zhu, Ping; Garcia‐Manero, Guillermo; Furman, Richard R.; Yu, Lihua; Smith, Peter G.; Buonamici, Silvia

doi:10.1016/j.celrep.2015.09.053

Cited by 373 publications

(548 citation statements)

References 48 publications

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“…(D) Intron mutations that reduce pairing with U2 snRNA (U257C and A258C) are sensitive to hsh155 mutations analogous to those found in human disease, whereas the 5 ′ SS, 3 ′ SS, and branch nucleophile mutations are not. Darman et al 2015;DeBoever et al 2015;Alsafadi et al 2016), similar to prp5 mutants in yeast (Xu and Query 2007).…”

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confidence: 82%

“…Disease-related mutations cluster in proteins involved in spliceosome assembly, particularly ones important for intron recognition, such as SF3B1 (also known as SAP155, SF3b155, and Hsh155p), SRSF1, and U2AF (Yoshida et al 2011;Quesada et al 2012). In disease-related SF3B1 mutants, changes in branch site (BS) usage have been identified (Darman et al 2015;Alsafadi et al 2016;Kesarwani et al 2016); however, the mechanisms by which these mutations affect splicing are largely unknown.…”

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confidence: 99%

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SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

et al. 2016

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Mutations in the U2 snRNP component SF3B1 are prominent in myelodysplastic syndromes (MDSs) and other cancers and have been shown recently to alter branch site (BS) or 3 ′ splice site selection in splicing. However, the molecular mechanism of altered splicing is not known. We show here that hsh155 mutant alleles in Saccharomyces cerevisiae, counterparts of SF3B1 mutations frequently found in cancers, specifically change splicing of suboptimal BS pre-mRNA substrates. We found that Hsh155p interacts directly with Prp5p, the first ATPase that acts during spliceosome assembly, and localized the interacting regions to HEAT (Huntingtin, EF3, PP2A, and TOR1) motifs in SF3B1 associated with disease mutations. Furthermore, we show that mutations in these motifs from both human disease and yeast genetic screens alter the physical interaction with Prp5p, alter branch region specification, and phenocopy mutations in Prp5p. These and other data demonstrate that mutations in Hsh155p and Prp5p alter splicing because they change the direct physical interaction between Hsh155p and Prp5p. This altered physical interaction results in altered loading (i.e., "fidelity") of the BS-U2 duplex into the SF3B complex during prespliceosome formation. These results provide a mechanistic framework to explain the consequences of intron recognition and splicing of SF3B1 mutations found in disease.

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confidence: 82%

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confidence: 99%

SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

et al. 2016

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“…Interestingly, since submission of our work, Darman et al reported findings fully confirming our results. They also showed the consequences of SF3B1 mutations on transcription through the generation of nonsense-mediated mRNA decay-sensitive aberrant spliced transcripts 23 .…”

Section: Discussionmentioning

confidence: 99%

Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage

Alsafadi¹,

Houy²,

Battistella³

et al. 2016

European Journal of Cancer

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Hotspot mutations in the spliceosome gene SF3B1 are reported in B20% of uveal melanomas. SF3B1 is involved in 3 0 -splice site (3 0 ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1 R625/K666 mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3 0 ss. Modelling the differential junctions in SF3B1 WT and SF3B1 R625/K666 cell lines demonstrates that the deregulated splice pattern strictly depends on SF3B1 status and on the 3'ss-sequence context. SF3B1 WT knockdown or overexpression do not reproduce the SF3B1 R625/K666 splice pattern, qualifying SF3B1 R625/K666 as change-of-function mutants. Mutagenesis of predicted branchpoints reveals that the SF3B1 R625/K666 -promoted splice pattern is a direct result of alternative branchpoint usage. Altogether, this study provides a better understanding of the mechanisms underlying splicing alterations induced by mutant SF3B1 in cancer, and reveals a role for alternative branchpoints in disease.

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“…Most mutations are missense mutations localized within the HEAT domain repeats lying in the carboxyterminal moiety of the protein, indicating a gain of function. Indeed, SF3B1 mutations in various cellular contexts are associated with abnormal splice events [51], which result from promotion of alternative branchpoint usage [52][53][54] (Fig. 2).…”

Section: Mutations Of the Sf3b1 Gene And Rna Biologymentioning

confidence: 99%

Chronic lymphocytic leukemia: Time to go past genomics?

2016

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Recent advances in massively parallel sequencing technologies have provided a detailed picture of the mutational landscape in CLL and underscored the vast degree of interpatient and intratumor heterogeneities. These studies have led to the characterization of novel putative driver genes and recurrently affected biological pathways, and to the modeling of CLL clonal evolution. We herein review selected aspects including recent advances in the biology of CLL and present cellular and biological processes involved in the development of CLL and potentially other mature B-cell lymphoproliferative neoplasms.

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Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point

Cited by 373 publications

References 48 publications

SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage

Chronic lymphocytic leukemia: Time to go past genomics?

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