Abstract
SR proteins are a class of RNA-binding proteins whose RNA-binding ability is required for both constitutive and alternative splicing. While members of the SR protein family were once thought to have redundant functions, in-depth biochemical analysis of their RNA-binding abilities has revealed distinct binding profiles for each SR protein, that often lead to either synergistic or antagonistic functions. SR protein family members SRSF1 and SRSF2 are two of the most highly studied RNA-binding proteins. Here we examine the various methods used to differentiate SRSF1 and SRSF2 RNA-binding ability. We discuss the benefits and type of information that can be determined using each method.
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References
Bandziulis RJ, Swanson MS, Dreyfuss G (1989) RNA-binding proteins as developmental regulators. Genes Dev 3:431–437
Kenan DJ, Query CC, Keene JD (1991) RNA recognition: towards identifying determinants of specificity. Trends Biochem Sci 16:214–220
Fu XD, Maniatis T (1990) Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343:437–441
Fu XD, Maniatis T (1992) The 35-kDa mammalian splicing factor SC35 mediates specific interactions between U1 and U2 small nuclear ribonucleoprotein particles at the 3′ splice site. Proc Natl Acad Sci U S A 89:1725–1729
Ge H, Manley JL (1990) A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell 62:25–34
Krainer AR, Conway GC, Kozak D (1990) Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes Dev 4:1158–1171
Spector DL, Fu XD, Maniatis T (1991) Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J 10:3467–3481
Fu XD (1993) Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365:82–85
Kohtz JD, Jamison SF, Will CL et al (1994) Protein-protein interactions and 5′-splice-site recognition in mammalian mRNA precursors. Nature 368:119–124
Wu JY, Maniatis T (1993) Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75:1061–1070
Fu XD, Maniatis T (1992) Isolation of a complementary DNA that encodes the mammalian splicing factor SC35. Science 256:535–538
Krainer AR, Maniatis T (1985) Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell 42:725–736
Fu XD, Mayeda A, Maniatis T et al (1992) General splicing factors SF2 and SC35 have equivalent activities in vitro, and both affect alternative 5′ and 3′ splice site selection. Proc Natl Acad Sci U S A 89:11224–11228
Mayeda A, Screaton GR, Chandler SD et al (1999) Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. Mol Cell Biol 19:1853–1863
Zahler AM, Lane WS, Stolk JA et al (1992) SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev 6:837–847
Caceres JF, Krainer AR (1993) Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO J 12:4715–4726
Ge H, Zuo P, Manley JL (1991) Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators. Cell 66:373–382
Krainer AR, Mayeda A, Kozak D et al (1991) Functional expression of cloned human splicing factor SF2: homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators. Cell 66:383–394
Zuo P, Manley JL (1993) Functional domains of the human splicing factor ASF/SF2. EMBO J 12:4727–4737
Sun Q, Mayeda A, Hampson RK et al (1993) General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev 7:2598–2608
Gallego ME, Gattoni R, Stevenin J et al (1997) The SR splicing factors ASF/SF2 and SC35 have antagonistic effects on intronic enhancer-dependent splicing of the beta-tropomyosin alternative exon 6A. EMBO J 16:1772–1784
Chandler SD, Mayeda A, Yeakley JM et al (1997) RNA splicing specificity determined by the coordinated action of RNA recognition motifs in SR proteins. Proc Natl Acad Sci U S A 94:3596–3601
Li X, Shambaugh ME, Rottman FM et al (2000) SR proteins Asf/SF2 and 9G8 interact to activate enhancer-dependent intron D splicing of bovine growth hormone pre-mRNA in vitro. RNA 6:1847–1858
Rooke N, Markovtsov V, Cagavi E et al (2003) Roles for SR proteins and hnRNP A1 in the regulation of c-src exon N1. Mol Cell Biol 23:1874–1884
Bourgeois CF, Popielarz M, Hildwein G et al (1999) Identification of a bidirectional splicing enhancer: differential involvement of SR proteins in 5′ or 3′ splice site activation. Mol Cell Biol 19:7347–7356
Arrisi-Mercado P, Romano M, Muro AF et al (2004) An exonic splicing enhancer offsets the atypical GU-rich 3′ splice site of human apolipoprotein A-II exon 3. J Biol Chem 279:39331–39339
Wang E, Huang Z, Hobson GM et al (2006) PLP1 alternative splicing in differentiating oligodendrocytes: characterization of an exonic splicing enhancer. J Cell Biochem 97:999–1016
Oliphant AR, Brandl CJ, Struhl K (1989) Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol 9:2944–2949
Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510
Tacke R, Manley JL (1995) The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J 14:3540–3551
Liu HX, Zhang M, Krainer AR (1998) Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev 12:1998–2012
Liu HX, Chew SL, Cartegni L et al (2000) Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Mol Cell Biol 20:1063–1071
Schaal TD, Maniatis T (1999) Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. Mol Cell Biol 19:1705–1719
Schaal TD, Maniatis T (1999) Multiple distinct splicing enhancers in the protein-coding sequences of a constitutively spliced pre-mRNA. Mol Cell Biol 19:261–273
Hallay H, Locker N, Ayadi L et al (2006) Biochemical and NMR study on the competition between proteins SC35, SRp40, and heterogeneous nuclear ribonucleoprotein A1 at the HIV-1 Tat exon 2 splicing site. J Biol Chem 281:37159–37174
Caputi M, Zahler AM (2002) SR proteins and hnRNP H regulate the splicing of the HIV-1 tev-specific exon 6D. EMBO J 21:845–855
Expert-Bezancon A, Sureau A, Durosay P et al (2004) hnRNP A1 and the SR proteins ASF/SF2 and SC35 have antagonistic functions in splicing of beta-tropomyosin exon 6B. J Biol Chem 279:38249–38259
Zahler AM, Damgaard CK, Kjems J et al (2004) 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. J Biol Chem 279:10077–10084
Gabut M, Mine M, Marsac C et al (2005) The SR protein SC35 is responsible for aberrant splicing of the E1alpha pyruvate dehydrogenase mRNA in a case of mental retardation with lactic acidosis. Mol Cell Biol 25:3286–3294
Solis AS, Peng R, Crawford JB et al (2008) Growth hormone deficiency and splicing fidelity: two serine/arginine-rich proteins, ASF/SF2 and SC35, act antagonistically. J Biol Chem 283:23619–23626
Mabon SA, Misteli T (2005) Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo. PLoS Biol 3, e374
Clery A, Sinha R, Anczukow O et al (2013) Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition. Proc Natl Acad Sci U S A 110:E2802–E2811
Phelan MM, Goult BT, Clayton JC et al (2012) The structure and selectivity of the SR protein SRSF2 RRM domain with RNA. Nucleic Acids Res 40:3232–3244
Tintaru AM, Hautbergue GM, Hounslow AM et al (2007) Structural and functional analysis of RNA and TAP binding to SF2/ASF. EMBO Rep 8:756–762
Pandit S, Zhou Y, Shiue L et al (2013) Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell 50:223–235
Spitzer J, Hafner M, Landthaler M et al (2014) PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins. Methods Enzymol 539:113–161
Huppertz I, Attig J, D'Ambrogio A et al (2014) iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65:274–287
Konig J, Zarnack K, Luscombe NM et al (2011) Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 13:77–83
Acknowledgment
L.S. was supported in part by H.N. & Frances Berger Foundation Fellowship and the Norman and Melinda Payson Fellowship. This work was supported by grants from the Beckman Research Institute to R.-J.L.
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Skrdlant, L., Lin, RJ. (2016). Characterization of RNA–Protein Interactions: Lessons from Two RNA-Binding Proteins, SRSF1 and SRSF2. In: Lin, RJ. (eds) RNA-Protein Complexes and Interactions. Methods in Molecular Biology, vol 1421. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3591-8_1
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DOI: https://doi.org/10.1007/978-1-4939-3591-8_1
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