Human Tra2 Proteins Are Sequence-Specific Activators of Pre-mRNA Splicing

The RNA-binding protein Tra2 is an important regulator of sex determination in Drosophila. Recently, two mammalian Tra2 homologs of unknown function have been described. Here, we show that human Tra2 proteins are present in HeLa cell nuclear extracts and that they bind efficiently and specifically to a previously characterized pre-mRNA splicing enhancer element. Indeed, both purified proteins bound preferentially to RNA sequences containing GAA repeats, characteristic of many enhancer elements. Neither Tra2 protein functioned in constitutive splicing in vitro, but both activated enhancer-dependent splicing in a sequence-specific manner and restored it after inhibition with competitor RNA. Our findings indicate that mammalian Tra2 proteins are sequence-specific splicing activators that likely participate in the control of cell-specific splicing patterns.

[1]  T. Maniatis,et al.  The role of specific protein-RNA and protein-protein interactions in positive and negative control of pre-mRNA splicing by Transformer 2 , 1994, Cell.

[2]  A. Zahler,et al.  Distinct functions of SR proteins in alternative pre-mRNA splicing. , 1993, Science.

[3]  B. S. Baker,et al.  The sex determination locus transformer-2 of Drosophila encodes a polypeptide with similarity to RNA binding proteins , 1989, Cell.

[4]  J. Manley,et al.  SR proteins and splicing control. , 1996, Genes & development.

[5]  Tom Maniatis,et al.  Specific interactions between proteins implicated in splice site selection and regulated alternative splicing , 1993, Cell.

[6]  A. Krainer,et al.  Functional expression of cloned human splicing factor SF2: homology to rna-binding proteins, U1 70K, and drosophila splicing regulators , 1991, Cell.

[7]  Xiang-Dong Fu,et al.  A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA , 1997, Nature.

[8]  I. Higuchi,et al.  Binding of the Drosophila transformer and transformer-2 proteins to the regulatory elements of doublesex primary transcript for sex-specific RNA processing. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[9]  T. Maniatis,et al.  A splicing enhancer exhibits both constitutive and regulated activities. , 1994, Genes & development.

[10]  S. Stamm,et al.  Molecular cloning of htra2-beta-1 and htra2-beta-2, two human homologs of tra-2 generated by alternative splicing. , 1997, DNA and cell biology.

[11]  T. Maniatis,et al.  The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. , 1996, Genes & development.

[12]  P. Sharp,et al.  Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. , 1994, Science.

[13]  M. Tohyama,et al.  Cloning of a Novel RNA Binding Polypeptide (RA301) Induced by Hypoxia/Reoxygenation (*) , 1995, The Journal of Biological Chemistry.

[14]  J. Steitz,et al.  SR proteins can compensate for the loss of U1 snRNP functions in vitro. , 1994, Genes & development.

[15]  Y. Shimura,et al.  The role of exon sequences in splice site selection. , 1993, Genes & development.

[16]  A. Zahler,et al.  A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer , 1995, Molecular and cellular biology.

[17]  A. Krainer,et al.  General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. , 1993, Genes & development.

[18]  Jeffrey C. Hall,et al.  Control of Male Sexual Behavior and Sexual Orientation in Drosophila by the fruitless Gene , 1996, Cell.

[19]  T. Maniatis,et al.  Positive control of pre-mRNA splicing in vitro. , 1992, Science.

[20]  F. Segade,et al.  Molecular cloning of a mouse homologue for the Drosophila splicing regulator Tra2 , 1996, FEBS letters.

[21]  A. Krainer,et al.  RNA splicing specificity determined by the coordinated action of RNA recognition motifs in SR proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[22]  SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT : TISSUE , .

[23]  T. Hazelrigg,et al.  Sex-specific processing of the Drosophila exuperantia transcript is regulated in male germ cells by the tra-2 gene. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. Valcárcel,et al.  The SR protein family: pleiotropic functions in pre-mRNA splicing. , 1996, Trends in biochemical sciences.

[25]  T. Maniatis,et al.  Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer. , 1996, Genes & development.

[26]  B. Dauwalder,et al.  A human homologue of the Drosophila sex determination factor transformer-2 has conserved splicing regulatory functions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[27]  H. Amrein,et al.  The sex-determining gene tra-2 of Drosophila encodes a putative RNA binding protein , 1988, Cell.

[28]  J. Manley,et al.  Primary structure of the human splicing factor asf reveals similarities with drosophila regulators , 1991, Cell.

[29]  Xiang-Dong Fu,et al.  The superfamily of arginine/serine-rich splicing factors. , 1995, RNA.

[30]  A. Krainer,et al.  Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. , 1994, Science.

[31]  A. Kornblihtt,et al.  A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP binding. , 1993, Genes & development.

[32]  Koji Kariya-city Aichi-pref. Tanaka,et al.  Polypurine sequences within a downstream exon function as a splicing enhancer , 1994, Molecular and cellular biology.

[33]  B. S. Baker,et al.  A negative feedback mechanism revealed by functional analysis of the alternative isoforms of the Drosophila splicing regulator transformer-2. , 1996, Genetics.

[34]  T Pawson,et al.  The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. , 1996, The EMBO journal.

[35]  K. Burtis,et al.  The regulation of sex determination and sexually dimorphic differentiation in Drosophila. , 1993, Current opinion in cell biology.

[36]  B. S. Baker,et al.  Sex and the single cell. I. On the action of major loci affecting sex determination in Drosophila melanogaster. , 1980, Genetics.

[37]  B. S. Baker,et al.  Autoregulation of the splicing of transcripts from the transformer-2 gene of Drosophila. , 1991, Genes & development.

[38]  M B Roth,et al.  SR proteins: a conserved family of pre-mRNA splicing factors. , 1992, Genes & development.

[39]  T. Maniatis,et al.  Synergistic interactions between two distinct elements of a regulated splicing enhancer. , 1995, Genes & development.

[40]  William Arbuthnot Sir Lane,et al.  A serine kinase regulates intracellular localization of splicing factors in the cell cycle , 1994, Nature.

[41]  M. Rosenfeld,et al.  A complex of nuclear proteins mediates SR protein binding to a purine-rich splicing enhancer. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[42]  A. Handyside,et al.  Sex and the single cell. , 1990, New scientist.

[43]  M. Garcia-Blanco,et al.  Protein–protein interactions and 5'-splice-site recognition in mammalian mRNA precursors , 1994, Nature.

[44]  B. S. Baker,et al.  Regulation of Sex-Specific Selection offruitless 5′ Splice Sites by transformerand transformer-2 , 1998, Molecular and Cellular Biology.

[45]  B. S. Baker,et al.  The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences. , 1995, The EMBO journal.

[46]  Xiang-Dong Fu Specific commitment of different pre-mRNAs to splicing by single SR proteins , 1993, Nature.

[47]  J. Manley,et al.  Overexpression of the SR proteins ASF/SF2 and SC35 influences alternative splicing in vivo in diverse ways. , 1995, RNA.

[48]  T. Cooper,et al.  The cardiac troponin T alternative exon contains a novel purine-rich positive splicing element , 1993, Molecular and cellular biology.

[49]  J. Lis,et al.  TheSRProtein B52/SRp55 IsEssential for Drosophila Development , 1994 .

[50]  T. Cooper,et al.  Muscle-specific splicing enhancers regulate inclusion of the cardiac troponin T alternative exon in embryonic skeletal muscle , 1996, Molecular and cellular biology.

[51]  J. Lis,et al.  The SR protein B52/SRp55 is essential for Drosophila development , 1994, Molecular and cellular biology.

[52]  T. Maniatis,et al.  A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA , 1993, Cell.

[53]  Stephen M. Mount,et al.  Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor , 1995, Molecular and cellular biology.

[54]  J. Manley,et al.  Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability. , 1996, Genes & development.

[55]  J. Manley,et al.  Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[56]  J. Manley,et al.  Phosphorylation of the ASF/SF2 RS domain affects both protein-protein and protein-RNA interactions and is necessary for splicing. , 1997, Genes & development.

[57]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[58]  Michael R. Green,et al.  The protein Sex-lethal antagonizes the splicing factor U2AF to regulate alternative splicing of transformer pre-mRNA , 1993, Nature.

[59]  I. Higuchi,et al.  Control of doublesex alternative splicing by transformer and transformer-2 in Drosophila , 1991, Science.

[60]  J. Manley,et al.  The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. , 1995, The EMBO journal.

[61]  A. Krainer,et al.  Identification and characterization of three members of the human SR family of pre‐mRNA splicing factors. , 1995, The EMBO journal.

[62]  M. Mckeown,et al.  att, a target for regulation by tra2 in the testes of Drosophila melanogaster, encodes alternative RNAs and alternative proteins , 1996, Molecular and cellular biology.

[63]  T. Cooper,et al.  A Short Sequence within Two Purine-Rich Enhancers Determines 5′ Splice Site Specificity , 1998, Molecular and Cellular Biology.

[64]  E. Birney,et al.  Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. , 1993, Nucleic acids research.

[65]  M. Rosenfeld,et al.  Control of calcitonin/calcitonin gene-related peptide pre-mRNA processing by constitutive intron and exon elements , 1993, Molecular and cellular biology.

[66]  K. Inoue Binding of the Drosophila transformer-2 proteins to the regulatory elements of doublesex primary transcript for sex-specific RNA processing , 1992 .

[67]  M B Roth,et al.  A conserved family of nuclear phosphoproteins localized to sites of polymerase II transcription , 1991, The Journal of cell biology.