Building specificity with nonspecific RNA-binding proteins

Specificity is key to biological regulation. Two families of RNA binding proteins, heterogeneous nuclear ribonucleoproteins and serine-arginine–rich proteins, were initially thought to have redundant or nonspecific biochemical functions. Recently, members of these families have been found as components of distinct regulatory complexes with highly specific and essential roles in mRNA metabolism. Here we discuss the basis for their functional specificity and the mechanisms of action of some of their characteristic protein domains.

[1]  J. Manley,et al.  RNA polymerase II and the integration of nuclear events. , 2000, Genes & development.

[2]  Adrian R. Krainer,et al.  Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2 , 1992, Cell.

[3]  B. Graveley Alternative splicing: increasing diversity in the proteomic world. , 2001, Trends in genetics : TIG.

[4]  R. Darnell,et al.  Sequence-Specific RNA Binding by a Nova KH Domain Implications for Paraneoplastic Disease and the Fragile X Syndrome , 2000, Cell.

[5]  A. Krainer,et al.  Involvement of SR proteins in mRNA surveillance. , 2004, Molecular cell.

[6]  H. Le Hir,et al.  Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions. , 2000, Genes & development.

[7]  R. Amann,et al.  Predictive Identification of Exonic Splicing Enhancers in Human Genes , 2022 .

[8]  C. Guthrie,et al.  Mechanical Devices of the Spliceosome: Motors, Clocks, Springs, and Things , 1998, Cell.

[9]  B. Blencowe Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. , 2000, Trends in biochemical sciences.

[10]  A. Kornblihtt,et al.  Alternative splicing: multiple control mechanisms and involvement in human disease. , 2002, Trends in genetics : TIG.

[11]  Gene W. Yeo,et al.  Systematic Identification and Analysis of Exonic Splicing Silencers , 2004, Cell.

[12]  J. Steitz,et al.  A molecular link between SR protein dephosphorylation and mRNA export. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  J. Manley,et al.  Phosphorylation–dephosphorylation differentially affects activities of splicing factor ASF/SF2 , 1998, The EMBO journal.

[14]  C. Schütt,et al.  Structure, function and evolution of sex-determining systems in Dipteran insects. , 2000, Development.

[15]  A. Krainer,et al.  Substrate Specificities of SR Proteins in Constitutive Splicing Are Determined by Their RNA Recognition Motifs and Composite Pre-mRNA Exonic Elements , 1999, Molecular and Cellular Biology.

[16]  G. Clore,et al.  Molecular basis of sequence‐specific single‐stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single‐stranded DNA , 2002, The EMBO journal.

[17]  Melissa J. Moore,et al.  Intron recognition comes of AGe , 2000, Nature Structural Biology.

[18]  M. Adams,et al.  The KH-type RNA-binding protein PSI is required for Drosophila viability, male fertility, and cellular mRNA processing. , 2002, Genes & development.

[19]  T. Cooper,et al.  Identification of a new class of exonic splicing enhancers by in vivo selection , 1997, Molecular and cellular biology.

[20]  J. Manley,et al.  Determinants of SR protein specificity. , 1999, Current opinion in cell biology.

[21]  Michael R. Green,et al.  Interaction of U2AF65 RS Region with Pre-mRNA of Branch Point and Promotion Base Pairing with U2 snRNA , 1996, Science.

[22]  B. Chabot,et al.  High-affinity hnRNP A1 binding sites and duplex-forming inverted repeats have similar effects on 5' splice site selection in support of a common looping out and repression mechanism. , 2002, RNA.

[23]  Elmar Wahle,et al.  Messenger RNA Turnover in Eukaryotes: Pathways and Enzymes , 2004, Critical reviews in biochemistry and molecular biology.

[24]  A. Kornblihtt,et al.  Multiple links between transcription and splicing. , 2004, RNA.

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

[26]  A. Krainer,et al.  Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. , 1999, Genes & development.

[27]  A. Krainer,et al.  Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1 , 2002, Nature Genetics.

[28]  G. Westerveld,et al.  Heterogeneous nuclear ribonucleoprotein G-T (HNRNP G-T) mutations in men with impaired spermatogenesis. , 2004, Molecular human reproduction.

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

[30]  D. Black Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.

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

[32]  P. Herrlich,et al.  Signal-dependent regulation of splicing via phosphorylation of Sam68 , 2002, Nature.

[33]  D. Black,et al.  A CaMK IV responsive RNA element mediates depolarization-induced alternative splicing of ion channels , 2001, Nature.

[34]  G. Orphanides,et al.  A Unified Theory of Gene Expression , 2002, Cell.

[35]  M. Perutz Polar zippers: their role in human disease. , 1995, Protein science : a publication of the Protein Society.

[36]  Michael R Green,et al.  A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. , 2004, Molecular cell.

[37]  N. Gray,et al.  A novel role for shuttling SR proteins in mRNA translation. , 2004, Genes & development.

[38]  P. Sharp,et al.  Splicing of precursors to mRNAs by the spliceosomes , 1993 .

[39]  G. Varani,et al.  Protein and RNA dynamics play key roles in determining the specific recognition of GU-rich polyadenylation regulatory elements by human Cstf-64 protein. , 2005, Journal of molecular biology.

[40]  J. Steitz,et al.  SR splicing factors serve as adapter proteins for TAP-dependent mRNA export. , 2003, Molecular cell.

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

[42]  A. Zahler,et al.  SC35 and Heterogeneous Nuclear Ribonucleoprotein A/B Proteins Bind to a Juxtaposed Exonic Splicing Enhancer/Exonic Splicing Silencer Element to Regulate HIV-1 tat Exon 2 Splicing* , 2004, Journal of Biological Chemistry.

[43]  M. Swanson,et al.  hnRNP complexes: composition, structure, and function. , 1999, Current opinion in cell biology.

[44]  J. Cáceres,et al.  Functional characterization of SR and SR‐related genes in Caenorhabditis elegans , 2000, The EMBO journal.

[45]  Xiang-Dong Fu,et al.  ASF/SF2-Regulated CaMKIIδ Alternative Splicing Temporally Reprograms Excitation-Contraction Coupling in Cardiac Muscle , 2005, Cell.

[46]  A. Aguilera Cotranscriptional mRNP assembly: from the DNA to the nuclear pore. , 2005, Current opinion in cell biology.

[47]  I. Higuchi,et al.  Control of Drosophila Sex-lethal pre-mRNA splicing by its own female-specific product. , 1992, Nucleic acids research.

[48]  E. Wagner,et al.  Polypyrimidine Tract Binding Protein Antagonizes Exon Definition , 2001, Molecular and Cellular Biology.

[49]  G. Dreyfuss,et al.  Structure of the Y14-Magoh Core of the Exon Junction Complex , 2003, Current Biology.

[50]  D L Black,et al.  Multisite RNA binding and release of polypyrimidine tract binding protein during the regulation of c-src neural-specific splicing. , 2000, Molecular cell.

[51]  N. Kataoka,et al.  SR proteins preferentially associate with mRNAs in the nucleus and facilitate their export to the cytoplasm , 2004, Genes to cells : devoted to molecular & cellular mechanisms.

[52]  J. Manley,et al.  A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy , 2003, Nature Genetics.

[53]  J. C. Clemens,et al.  Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity , 2000, Cell.

[54]  Ravinder Singh,et al.  Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding. , 2003, RNA.

[55]  C. Shin,et al.  Dephosphorylated SRp38 acts as a splicing repressor in response to heat shock , 2004, Nature.

[56]  A. Krainer,et al.  Nuclear Export and Retention Signals in the RS Domain of SR Proteins , 2002, Molecular and Cellular Biology.

[57]  A. Krainer,et al.  Pre-mRNA splicing in the new millennium. , 2001, Current opinion in cell biology.

[58]  J. Manley,et al.  Genetic analysis of the SR protein ASF/SF2: interchangeability of RS domains and negative control of splicing. , 1998, Genes & development.

[59]  G. Varani,et al.  Recent advances in RNA-protein recognition. , 2001, Current opinion in structural biology.

[60]  J. Kjems,et al.  hnRNP A1 controls HIV-1 mRNA splicing through cooperative binding to intron and exon splicing silencers in the context of a conserved secondary structure. , 2002, RNA.

[61]  Michael R. Green,et al.  A Novel Peptide Recognition Mode Revealed by the X-Ray Structure of a Core U2AF35/U2AF65 Heterodimer , 2001, Cell.

[62]  B. Graveley Sorting out the complexity of SR protein functions. , 2000, RNA.

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

[64]  J. Valcárcel,et al.  The hnRNP A1 protein regulates HIV‐1 tat splicing via a novel intron silencer element , 2001, The EMBO journal.

[65]  B. Dauwalder,et al.  Analysis of the functional specificity of RS domains in vivo , 1998, The EMBO journal.

[66]  R. Reed,et al.  Coupling transcription, splicing and mRNA export. , 2003, Current opinion in cell biology.

[67]  Michael Sattler,et al.  Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. , 2003, Molecular cell.

[68]  A. Krainer,et al.  Listening to silence and understanding nonsense: exonic mutations that affect splicing , 2002, Nature Reviews Genetics.

[69]  P. Zamore,et al.  RNA annealing activity is intrinsically associated with U2AF. , 1993, The Journal of biological chemistry.

[70]  O. Kent,et al.  Structuring of the 3′ Splice Site by U2AF65* , 2003, Journal of Biological Chemistry.

[71]  Hang Shi,et al.  Crystal structure of the Drosophila Mago nashi-Y14 complex. , 2003, Genes & development.

[72]  A. Krainer,et al.  The Mkk3/6-p38–Signaling Cascade Alters the Subcellular Distribution of Hnrnp A1 and Modulates Alternative Splicing Regulation , 2000, The Journal of cell biology.

[73]  M. Wollerton,et al.  Polypyrimidine Tract Binding Protein Modulates Efficiency of Polyadenylation , 2004, Molecular and Cellular Biology.

[74]  Melissa S Jurica,et al.  Pre-mRNA splicing: awash in a sea of proteins. , 2003, Molecular cell.

[75]  A. Krainer,et al.  Pre-mRNA splicing in the absence of an SR protein RS domain. , 2000, Genes & development.

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

[77]  G. Dreyfuss,et al.  Messenger-RNA-binding proteins and the messages they carry , 2002, Nature Reviews Molecular Cell Biology.

[78]  T. Maniatis,et al.  A systematic analysis of the factors that determine the strength of pre‐mRNA splicing enhancers , 1998, The EMBO journal.

[79]  J. Valcárcel,et al.  Alternative pre-mRNA splicing: the logic of combinatorial control. , 2000, Trends in biochemical sciences.

[80]  A. Krainer,et al.  Decrease in hnRNP A/B expression during erythropoiesis mediates a pre‐mRNA splicing switch , 2002, The EMBO journal.

[81]  A. Krainer,et al.  Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. , 2001, Molecular cell.

[82]  C. Shin,et al.  Cell signalling and the control of pre-mRNA splicing , 2004, Nature Reviews Molecular Cell Biology.

[83]  D. Black,et al.  Protein kinase A phosphorylation modulates transport of the polypyrimidine tract-binding protein , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[84]  J. Valcárcel,et al.  Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. , 1995, Science.

[85]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

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

[87]  Elisa Izaurralde,et al.  The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3 , 2004, Nature Structural &Molecular Biology.

[88]  Massimo Caputi,et al.  SR proteins and hnRNP H regulate the splicing of the HIV‐1 tev‐specific exon 6D , 2002, The EMBO journal.

[89]  G. Clore,et al.  Structure and dynamics of KH domains from FBP bound to single-stranded DNA , 2002, Nature.

[90]  C. Shin,et al.  The SR Protein SRp38 Represses Splicing in M Phase Cells , 2002, Cell.

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

[92]  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.

[93]  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.

[94]  M. Green,et al.  Pre-mRNA splicing of IgM exons M1 and M2 is directed by a juxtaposed splicing enhancer and inhibitor. , 1999, Genes & development.

[95]  T. Nilsen The spliceosome: no assembly required? , 2002, Molecular cell.

[96]  A. Krainer,et al.  A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. , 1998, Genes & development.

[97]  J. Tazi,et al.  Phosphorylation-dependent control of the pre-mRNA splicing machinery. , 2003, Progress in molecular and subcellular biology.

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

[99]  S Cusack,et al.  Crystal structure of the human nuclear cap binding complex. , 2001, Molecular cell.

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

[101]  B R Franza,et al.  Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors. , 1998, RNA.

[102]  M. Hentze,et al.  Molecular mechanisms of translational control , 2004, Nature Reviews Molecular Cell Biology.

[103]  P. Grabowski,et al.  Coordinate repression of a trio of neuron-specific splicing events by the splicing regulator PTB. , 1999, RNA.

[104]  Michael R. Green,et al.  Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. , 2004, Molecular cell.

[105]  D. Gatfield,et al.  A novel mode of RBD-protein recognition in the Y14–Mago complex , 2003, Nature Structural Biology.

[106]  Michael R. Green,et al.  U2AF homology motifs: protein recognition in the RRM world. , 2004, Genes & development.

[107]  G. C. Roberts,et al.  Smooth muscle‐specific switching of alpha‐tropomyosin mutually exclusive exon selection by specific inhibition of the strong default exon. , 1994, The EMBO journal.

[108]  Ravinder Singh,et al.  Drosophila polypyrimidine‐tract binding protein (PTB) functions specifically in the male germline , 2003, The EMBO journal.

[109]  D. Rio,et al.  Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing. , 1995, Genes & development.

[110]  N. Grishin,et al.  KH domain: one motif, two folds. , 2001, Nucleic acids research.

[111]  Bosiljka Tasic,et al.  Alternative pre-mRNA splicing and proteome expansion in metazoans , 2002, Nature.

[112]  Kazuki Kurimoto,et al.  Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein , 1999, Nature.

[113]  A. Krainer,et al.  Selection of Alternative 5′ Splice Sites: Role of U1 snRNP and Models for the Antagonistic Effects of SF2/ASF and hnRNP A1 , 2000, Molecular and Cellular Biology.

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

[115]  J. Valcárcel,et al.  Splicing regulation in Drosophila sex determination. , 2003, Progress in molecular and subcellular biology.

[116]  Philip R. Evans,et al.  Crystal structure of the spliceosomal U2B″–U2A′ protein complex bound to a fragment of U2 small nuclear RNA , 1998, Nature.

[117]  J. Castle,et al.  Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays , 2003, Science.