title: U2AF1 mutations alter splice site recognition in hematological malignancies.
abstract: 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.
authors.affiliation: Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
authors.forename: Janine O
authors.initials: JO
authors.lastname: Ilagan
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Division of Medical Oncology, School of Medicine, University of Washington, Seattle, Washington 98109, USA.
authors.forename: Aravind
authors.initials: A
authors.lastname: Ramakrishnan
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
authors.forename: Brian
authors.initials: B
authors.lastname: Hayes
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
authors.forename: Michele E
authors.initials: ME
authors.lastname: Murphy
authors.affiliation: Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
authors.forename: Ahmad S
authors.initials: AS
authors.lastname: Zebari
authors.affiliation: Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; rbradley@fhcrc.org.
authors.forename: Philip
authors.initials: P
authors.lastname: Bradley
authors.affiliation: Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; rbradley@fhcrc.org.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Bradley
mesh_terms: D017209:Apoptosis; D064007:Ataxia Telangiectasia Mutated Proteins / Q000235:genetics / Q000378:metabolism; D053181:Caspase 8 / Q000235:genetics / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism; D004249:DNA Damage; D019175:DNA Methylation; D052217:Fanconi Anemia Complementation Group A Protein / Q000235:genetics / Q000378:metabolism; D019337:Hematologic Neoplasms / Q000235:genetics* / Q000473:pathology; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D020014:K562 Cells; D008958:Models, Molecular; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D022821:RNA Splice Sites; D012326:RNA Splicing; D012261:Ribonucleoproteins / Q000235:genetics* / Q000378:metabolism; D000072668:Splicing Factor U2AF; D016335:Zinc Fingers; D000097584:DNA Methyltransferase 3B
chemical_list: D064007:Ataxia Telangiectasia Mutated Proteins; D053181:Caspase 8; D004248:DNA (Cytosine-5-)-Methyltransferases; D052217:Fanconi Anemia Complementation Group A Protein; D006657:Histones; D009687:Nuclear Proteins; D022821:RNA Splice Sites; D012261:Ribonucleoproteins; D000072668:Splicing Factor U2AF; D000097584:DNA Methyltransferase 3B; C498471:FANCA protein, human; C430886:MACROH2A2 protein, human; C076753:U2AF1 protein, human; C576597:ATR protein, human; C505530:CASP8 protein, human