Allele-Specific Effects of U2AF1 Mutations on Alternative Splicing

Date of Award

Winter 12-15-2013

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Cell Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Myelodysplastic syndromes (MDS) are a heterogenous group of hematopoietic stem cell disorders characterized by dysplastic blood cell formation and peripheral blood cytopenias. Up to 30% of patients with MDS will progress to a highly chemotherapy-resistant secondary acute myeloid leukemia (sAML). Four independent groups, including ours, have previously discovered spliceosome mutations in MDS samples using unbiased sequencing approaches (up to 57% of patients carry a mutation in 1 of 8 spliceosome genes). We used whole genome sequencing to identify novel mutations in the genomes of 15 patients with secondary AML that had progressed from de novo MDS and identified a novel recurrent point mutation affecting the same codon (serine at amino acid position 34) in the U2AF1 gene in 3/15 samples. Using total exonic resequencing of U2AF1 in 150 de novo MDS samples, we identified mutations affecting the S34 and Q157 codons in 18/150 (11%) samples. Apart from our group, recent reports have also confirmed the presence of U2AF1 mutations in MDS and AML patients; S34F, S34Y, Q157R and Q157P. Although the role of U2AF1 as an accessory factor in the U2 snRNP is well established, it is not yet clear how these mutations affect splicing or contribute to MDS. We found that recurrent mutations in U2AF1 have allele-specific effects on alternative splicing (AS). U2AF1 (S34F) localizes normally within the nuclear speckles and co-localizes with U2AF2. However, the direct interaction of U2AF1 (S34F) with other components of the spliceosome is reduced. The global gene expression pattern of CD34+ hematopoietic cells defined by RNA-seq is not perturbed by U2AF1 (S34F); however, analysis of splice junctions revealed significant differences in the abundance of known and novel junctions in samples transfected with U2AF1 (S34F). These differences reflected alterations in exon skipping, alternative site usage and other splicing events. For selected transcripts, splicing alterations detected by RNA-seq were confirmed by analysis of primary de novo MDS patient samples. These data suggest that the S34F mutation affects U2AF1 function, leading to aberrant AS of target genes, some of which may be relevant for MDS pathogenesis.


English (en)

Chair and Committee

Timothy A Graubert

Committee Members

Timothy A Graubert, Daniel Link, Grant Challen, Gerald Dorn, Rakesh Nagarajan, Jason Weber


Permanent URL: https://doi.org/10.7936/K7VT1Q1S

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