SF3b1 mutations associated with myelodysplastic syndromes alter the fidelity of branchsite selection in yeast

Carrocci, Tucker J.; Zoerner, Douglas M.; Paulson, Joshua C.; Hoskins, Aaron A.

doi:10.1093/nar/gkw1349

Cited by 66 publications

(131 citation statements)

References 70 publications

(111 reference statements)

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“…Recently, the DEAD-box RNP-unwindase PRP5 (also called DDX46) was found to interact genetically and physically with the yeast SF3B1 homologue (called HSH155), and hotspot mutations altered this interaction [85, 86]. Considering SF3B1–RNA contacts, an appropriate conformation of the SF3B1–pre-mRNA complex could serve as a checkpoint for the ATPase activity of PRP5, which is required for stable association of the U2 snRNA with the BPS.…”

Section: Discussionmentioning

confidence: 99%

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures

Jenkins

Kielkopf

2017

Trends in Genetics

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Somatic mutations of pre-mRNA splicing factors recur among patients with myelodysplastic syndromes (MDS) and related malignancies. Although these MDS-relevant mutations alter splicing of a subset of transcripts, the mechanisms by which these single amino acid substitutions change gene expression remain controversial. New structures of spliceosome intermediates and associated protein complexes shed light on the molecular interactions mediated by “hotspots” of the SF3B1 and U2AF1 pre-mRNA splicing factors. The frequently mutated SF3B1 residues contact the pre-mRNA splice site. Based on structural-homology with other spliceosome subunits and recent findings of altered RNA binding by mutant U2AF1 proteins, we suggest that affected U2AF1 residues also contact pre-mRNA. Altered pre-mRNA recognition emerges as a molecular theme among MDS-relevant mutations of pre-mRNA splicing factors.

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Section: Discussionmentioning

confidence: 99%

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures

Jenkins

Kielkopf

2017

Trends in Genetics

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“…As noted earlier, RNA splicing alterations imparted by mutations in SF3B1, 12,15,17,18 SRSF2, 6,14 U2AF1, 10,11,20 and ZRSR2 19 are each distinct, and thus, it is not clear what precise splicing changes would be expected in MDS Figure 1 (continued) function required in every cell, overt phenotypic effects of these mutations are only apparent within the retina. In contrast to the U4/U6.U5 tri-snRNP mutations in autosomal dominant retinitis pigmentosa, mutations in the RNA splicing factors SF3B1, U2AF1, SRSF2, and ZRSR2 are enriched in leukemias and subsets of epithelial malignancies.…”

Section: Is Disruption Of Rna Splicing a Universal Disease Mechanism mentioning

confidence: 96%

How do messenger RNA splicing alterations drive myelodysplasia?

Joshi

Halene

Abdel-Wahab

2017

Blood

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Mutations in RNA splicing factors are the single most common class of genetic alterations in myelodysplastic syndrome (MDS) patients. Although much has been learned about how these mutations affect splicing at a global-and transcript-specific level, critical questions about the role of these mutations in MDS development and maintenance remain. Here we present the questions to be addressed in order to understand the unique enrichment of these mutations in MDS. (Blood. 2017; 129(18):2465-2470 IntroductionMyelodysplastic syndromes (MDSs) represent clonal disorders of hematopoietic stem cells (HSCs) whereby hematopoietic cell-intrinsic genetic alterations as well as non-cell autonomous factors contribute to an aberrant HSC that produces morphologically abnormal progeny and has impaired ability to generate mature blood cells. Due to the wide clinical and morphologic heterogeneity of MDS, substantial effort has been placed on characterizing the genetic alterations present in MDS cells in hopes of improving our ability to understand, diagnose, and treat the disease. Extensive targeted mutational analysis of protein coding genes has identified that MDS is characterized by a high frequency of mutations in genes encoding messenger RNA (mRNA) splicing factors as well as epigenetic modifiers.1-3 The discovery of mutations in RNA splicing factors in particular was quite unexpected as these mutations are generally uncommon in cancer yet are present in 50% to 60% of MDS patients. Interestingly, there are clear associations between specific mutated splicing factors and subtypes of MDS, most notably mutations in the RNA splicing factor SF3B1 in .90% of patients with MDS with ring sideroblasts.1,2,4 Moreover, the nature of these mutations is quite conspicuous as they occur as heterozygous point mutations at highly recurrent residues. Finally, within MDS patients, these mutations are almost always mutually exclusive; an MDS patient almost never has .1 RNA splicing factor mutation at the same time [1][2][3] (although rare individuals with mutations in .1 RNA splicing factor have been noted, 5 these occur far less frequently than expected by chance in MDS and it is unclear if both mutations in such cases are present within the same cell and/or how the mutations may impact splicing if coexpressed in the same cell).The discovery of RNA splicing factor mutations has led to intense efforts to understand their biological impact on hematopoiesis, 6-9 their genomic and biochemical effects on RNA splicing, 10-21 their structural effects, 22 and potential means to therapeutically target cells bearing these mutations. 8,[23][24][25] Although there have been major advances in understanding the role of RNA splicing factor mutations in MDS pathogenesis and therapy (as reviewed recently [26][27][28] ), major questions about their biological consequences within cells, requirement in disease initiation vs maintenance, and cell autonomous vs nonautonomous roles remain. In addition, numerous questions about the structural and biochemical effects of...

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“…In Cus2 these are an acidic residue (D204) important for salt-bridge formation, and a conserved phenylalanine (F235) important for stacking interactions. Although a ULM-containing binding partner of Cus2 has not been identified, Cus2 is reported to interact with the U2 snRNP protein Hsh155 in two-hybrid experiments (Perriman and Ares 2000;Yu et al 2008;Carrocci et al 2017). Hsh155 is homologous to human SF3b1 (Pauling et al 2000), which contains at least five ULMs in its N-terminal sequences (Thickman et al 2006) (Fig.…”

Section: Identification Of a Potential Uhm-ulm Interaction Between Cumentioning

confidence: 99%

Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction

Talkish

Igel

Hunter

et al. 2019

Preprint

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Stable recognition of the intron branchpoint by the U2 snRNP to form the prespliceosome is the first ATP-dependent step of splicing. Genetic and biochemical data from yeast indicate that Cus2 aids U2 snRNA folding into the stem IIa conformation prior to pre-spliceosome formation. Cus2 must then be removed by an ATP-dependent function of Prp5 before assembly can progress. However, the location from which Cus2 is displaced and the nature of its binding to the U2 snRNP are unknown. Here, we show that Cus2 contains a conserved UHM (U2AF homology motif) that binds Hsh155, the yeast homolog of human SF3b1, through a conserved ULM (U2AF ligand motif).Mutations in either motif block binding and allow pre-spliceosome formation without ATP. A 2.0 Å resolution structure of the Hsh155 ULM in complex with the UHM of Tat-SF1, the human homolog of Cus2, and complementary binding assays show that the interaction is highly similar between yeast and humans. Furthermore, we show that Tat-SF1 can replace Cus2 function by enforcing ATP-dependence of pre-spliceosome formation in yeast extracts. Cus2 is removed before pre-spliceosome formation, and both Cus2 and its Hsh155 ULM binding site are absent from available cryo-EM structure models. However, our data are consistent with the apparent location of the disordered Hsh155 ULM between the U2 stem-loop IIa and the HEAT-repeats of Hsh155 that interact with Prp5. We propose a model in which Prp5 uses ATP to remove Cus2 from Hsh155 such that extended base pairing between U2 snRNA and the intron branchpoint can occur.

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SF3b1 mutations associated with myelodysplastic syndromes alter the fidelity of branchsite selection in yeast

Cited by 66 publications

References 70 publications

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures

How do messenger RNA splicing alterations drive myelodysplasia?

Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction

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