title: The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation.
abstract: Alternative pre-mRNA splicing is a prevalent mechanism in mammals that promotes proteomic diversity, including expression of cell-type specific protein isoforms. We characterized a role for RBM38 (RNPC1) in regulation of alternative splicing during late erythroid differentiation. We used an Affymetrix human exon junction (HJAY) splicing microarray to identify a panel of RBM38-regulated alternatively spliced transcripts. Using microarray databases, we noted high RBM38 expression levels in CD71(+) erythroid cells and thus chose to examine RBM38 expression during erythroid differentiation of human hematopoietic stem cells, detecting enhanced RBM38 expression during late erythroid differentiation. In differentiated erythroid cells, we validated a subset of RBM38-regulated splicing events and determined that RBM38 regulates activation of Protein 4.1R (EPB41) exon 16 during late erythroid differentiation. Using Epb41 minigenes, Rbm38 was found to be a robust activator of exon 16 splicing. To further address the mechanism of RBM38-regulated alternative splicing, a novel mammalian protein expression system, followed by SELEX-Seq, was used to identify a GU-rich RBM38 binding motif. Lastly, using a tethering assay, we determined that RBM38 can directly activate splicing when recruited to a downstream intron. Together, our data support the role of RBM38 in regulating alternative splicing during erythroid differentiation.
authors.affiliation: Department of Medicine (Hematology-Oncology Division), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Laurie A
authors.initials: LA
authors.lastname: Heinicke
authors.forename: Behnam
authors.initials: B
authors.lastname: Nabet
authors.forename: Shihao
authors.initials: S
authors.lastname: Shen
authors.forename: Peng
authors.initials: P
authors.lastname: Jiang
authors.forename: Sebastiaan
authors.initials: S
authors.lastname: van Zalen
authors.forename: Benjamin
authors.initials: B
authors.lastname: Cieply
authors.forename: J Eric
authors.initials: JE
authors.lastname: Russell
authors.forename: Yi
authors.initials: Y
authors.lastname: Xing
authors.forename: Russ P
authors.initials: RP
authors.lastname: Carstens
mesh_terms: D017398:Alternative Splicing; D001483:Base Sequence; D001665:Binding Sites; D002454:Cell Differentiation; D002478:Cells, Cultured; D017124:Conserved Sequence; D003598:Cytoskeletal Proteins / Q000235:genetics / Q000378:metabolism; D041905:Erythroid Cells / Q000378:metabolism*; D005091:Exons; D057809:HEK293 Cells; D006801:Humans; D061986:MCF-7 Cells; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000502:physiology*
chemical_list: D003598:Cytoskeletal Proteins; D008565:Membrane Proteins; C515435:RBM38 protein, human; D016601:RNA-Binding Proteins; C028841:erythrocyte membrane band 4.1 protein