Chromosoma

, Volume 113, Issue 5, pp 244–257 | Cite as

Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene

  • Xin Sun
  • Jian Zhao
  • Karin Kylberg
  • Teresa Soop
  • Kevin Palka
  • Erik Sonnhammer
  • Neus Visa
  • Alla T. Alzhanova-Ericsson
  • Bertil Daneholt
Research Article

Abstract

Chromosomal puffs on the polytene chromosomes in the dipteran Chironomus tentans offer the possibility of comparing the appearance of RNA-binding proteins at different transcription sites. We raised a monoclonal antibody that recognized a 130 kDa protein, designated hrp130. Immunocytological analysis of isolated chromosomes showed that hrp130 is heavily accumulated in a specific puff, called Balbiani ring 3; only occasionally is hrp130 abundant in one or two additional puffs on other chromosomes. The immunolabeling was sensitive to RNase treatment, suggesting that hrp130 is associated with nascent ribonucleoproteins. As shown by immunoelectron microscopy hrp130 is distributed along the active BR3 genes. The full sequence of hrp130 was determined by cDNA cloning. The protein comprises 1028 amino acids and contains three WW domains in the N-terminal half and six FF domains in the C-terminal half of the molecule. The protein is conserved from Caenorhabditis elegans to mammals; the human homolog is known as the transcription elongation repressor CA150. We propose that the abundance of hrp130/CA150 in BR3 is connected with the exceptionally high level of splicing in this locus and that hrp130/CA150 adjusts the transcription rate to the numerous splicing events taking place along the gene to ensure proper splicing.

References

  1. Abovich N, Rosbash M (1997) Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89:403–412CrossRefPubMedGoogle Scholar
  2. Aebi M, Weissman C (1987) Precision and orderliness in splicing. Trends Genet 3:102–107Google Scholar
  3. Allen M, Friedler A, Schon O, Bycroft M (2002) The structure of an FF domain from human HYPA/FB11. J Mol Biol 323:411–416CrossRefPubMedGoogle Scholar
  4. Alzhanova-Ericsson AT, Sun X, Visa N, Kiseleva E, Wurtz T, Daneholt B (1996) A protein of the SR family of splicing factors binds extensively to exonic Balbiani ring pre-mRNA and accompanies the RNA from the gene to the nuclear pore. Genes Dev 10:2881–2893PubMedGoogle Scholar
  5. Baurén G, Belikov S, Wieslander L (1998) Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3′-end formation and excision of the 3′-terminal intron. Genes Dev 12:2759–2769PubMedGoogle Scholar
  6. Bedford MT, Leder P (1999) The FF domain: a novel motif that often accompanies WW domains. Trends Biochem Sci 24:264–265CrossRefPubMedGoogle Scholar
  7. Beford MT, Chan DC, Leder P (1997) FBP WW domains and the Abl SH3 domain bind to a specific class of proline-rich ligands. EMBO J 16:2376–2383CrossRefPubMedGoogle Scholar
  8. Bentley D (1999) Coupling RNA polymerase II transcription with pre-mRNA processing. Curr Opin Cell Biol 11:347–351CrossRefPubMedGoogle Scholar
  9. Björkroth B, Ericsson C, Lamb MM, Daneholt B (1988) Structure of the chromatin axis during transcription. Chromosoma 96:333–340Google Scholar
  10. Bohne J, Cole SE, Sune C, Lindman BR, Ko VD, Vogt TF, Garcia-Blanco MA (2000) Expression analysis and mapping of the mouse and human transcriptional regulator CA150. Mamm Genome 11:930–933CrossRefPubMedGoogle Scholar
  11. Burd CG, Dreyfuss G (1994) Conserved structures and diversity of functions of RNA-binding proteins. Science 265:615–621PubMedGoogle Scholar
  12. Carty SM, Goldstrohm AC, Sune C, Garcia-Blanco MA, Greenleaf A (2000) Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II. Proc Natl Acad Sci USA 97:9015–9020CrossRefGoogle Scholar
  13. Chen HI, Sudol M (1995) The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules. Proc Natl Acad Sci USA 92:7819–7823PubMedGoogle Scholar
  14. Daneholt B (2001) Assembly and transport of a premessenger RNP particle. Proc Natl Acad Sci USA 98:7012–7017CrossRefGoogle Scholar
  15. Daneholt B, Edström J-E (1967) The content of deoxyribonucleic acid in individual polytene chromosomes of Chironomus tentans. Cytogenetics 6:350–356PubMedGoogle Scholar
  16. Dignam SS, Case ST (1990) Balbiani ring 3 in Chironomus tentans encodes a 185-kDa secretory protein which is synthesized throughout the fourth larval instar. Gene 88:133–140CrossRefPubMedGoogle Scholar
  17. Dreyfuss G, Matunis MJ, Pinol Roma S, Burd CG (1993) hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 62:289–321CrossRefPubMedGoogle Scholar
  18. Ermekova KS, Zambrano N, Linn H, Minopoli G, Gertler F, Russo T, Sudol M (1998) The WW domain of neural protein FE65 interacts with proline-rich motifs in mena, the mammalian homolog of Drosophlia enabled. J Biol Chem 272:32869–32877Google Scholar
  19. Fakan S (1994) Perichromatin fibrils are in situ forms of nascent transcript. Trends Cell Biol 4:86–90CrossRefPubMedGoogle Scholar
  20. Goldstrohm AC, Albrecht TR, Sune C, Bedford MT, Garcia-Blanco MA (2001) The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1. Mol Cell Biol 21:7617–7628CrossRefPubMedGoogle Scholar
  21. Grasso C, Lee C (2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 20:1546–1556CrossRefPubMedGoogle Scholar
  22. Harlow E, Lane D (1988) Antibodies, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NYGoogle Scholar
  23. Hirose Y, Manley JL (2000) RNA polymerase II and the integration of nuclear events. Genes Dev 14:1415–1429PubMedGoogle Scholar
  24. Kabisch R, Bautz EKF (1983) Differential distribution of RNA polymerase B and nonhistone chromosomal proteins in polytene chromosomes of Drosophila melanogaster. EMBO J 2:395–402PubMedGoogle Scholar
  25. Kao HY, Siliciano PG (1996) Identification of Prp40, a novel essential yeast splicing factor associated with the U1 small nuclear ribonucleoprotein particle. Mol Cell Biol 16:960–967PubMedGoogle Scholar
  26. Kiseleva E, Wurtz T, Visa N, Daneholt B (1994) Assembly and disassembly of spliceosomes along a specific pre-messenger RNP fiber. EMBO J 13:6052–6061PubMedGoogle Scholar
  27. Krämer A, Utans U (1991) Three protein factors (SF1, SF3 and U2AF) function in pre-splicing complex formation in addition to snRNPs. EMBO J 10:1503–1509PubMedGoogle Scholar
  28. Krecic AM, Swanson MS (1999) hnRNP complexes: composition, structure, and function. Curr Opin Cell Biol 11:363–371CrossRefPubMedGoogle Scholar
  29. Lacroix JC, Azzouz R, Boucher D, Abbadie C, Pyne CK, Charlemagne J (1985) Monoclonal antibodies to lampbrush chromosome antigens of Pleurodeles waltlii. Chromosoma 92:69–80PubMedGoogle Scholar
  30. Lei EP, Krebber H, Silver PA (2001) Messenger RNAs are recruited for nuclear export during transcription. Genes Dev 15:1771–1782CrossRefPubMedGoogle Scholar
  31. Lezzi M, Meyer B, Mähr R (1981) Heat shock phenomena in Chironomus tentans I. In vivo effects of heat, overheat, and quenching on salivary chromosome puffing. Chromosoma 83:327–339PubMedGoogle Scholar
  32. Maniatis T, Reed R (2002) An extensive network of coupling among gene expression machines. Nature 416:499–506CrossRefPubMedGoogle Scholar
  33. Mattaj I (1993) RNA recognition: a family matter? Cell 73:837–840CrossRefPubMedGoogle Scholar
  34. Matunis EL, Matunis MJ, Dreyfuss G (1993) Association of individual hnRNP proteins and snRNPs with nascent transcripts. J Cell Biol 121:219–228CrossRefPubMedGoogle Scholar
  35. Morris DP, Greenleaf AL (2000) The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 275:39935–39943CrossRefPubMedGoogle Scholar
  36. Morris DP, Lee JM, Sterner DE, Brickey WJ, Greenleaf AL (1997) Assaying CTD kinases in vitro and phosphorylation-modulated properties of RNA polymerase II in vivo. Methods Companion Methods Enzymol 12:264–275CrossRefGoogle Scholar
  37. Neubauer G, Gottschalk A, Fabrizio P, Seraphin B, Lührmann R, Mann M (1997) Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci USA 94:385–390CrossRefGoogle Scholar
  38. Neubauer G, King A, Rappsilber J, Calvio C, Watson M, Ajuk P, Sleeman J, Lamond A, Mann M (1998) Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat Genet 20:46–50CrossRefPubMedGoogle Scholar
  39. Paulsson G, Lendahl U, Galli J, Ericsson C, Wieslander L (1990) The Balbiani ring 3 gene in Chironomus tentans has a diverged repetitive structure split by many introns. J Mol Biol 211:331–349PubMedGoogle Scholar
  40. Pelling C (1964) Ribonukleinsäure-Synthese der Riesenchromosomen. Autoradiographische Untersuchungen an Chironomus tentans. Chromosoma 15:71–122PubMedGoogle Scholar
  41. Pinol-Roma S, Choi YD, Matunis MJ, Dreyfuss G (1988) Immunopurification of heterogeneous nuclear ribonucleoprotein particles reveals an assortment of RNA-binding proteins. Genes Dev 2:215–227PubMedGoogle Scholar
  42. Pinol-Roma S, Swanson MS, Gall JG, Dreyfuss G (1989) A novel heterogeneous nuclear RNP protein with a unique distribution on nascent transcripts. J Cell Biol 109:2575–2587CrossRefPubMedGoogle Scholar
  43. Proudfoot NJ, Furger A, Dye MJ (2002) Integrating mRNA processing with transcription. Cell 108:501–512CrossRefPubMedGoogle Scholar
  44. Roth MB, Gall JG (1987) Monoclonal antibodies that recognize transcription unit proteins on newt lampbrush chromosomes. J Cell Biol 105:1047–1054CrossRefPubMedGoogle Scholar
  45. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  46. Sommerville J, Crichton C, Malcolm D (1978) Immunofluorescent localization of transcriptional activity on lampbrush chromosomes. Chromosoma 66:99–114Google Scholar
  47. Strässer K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, Rodriguez-Navarro S, Rondon AG, Aguilera A, Struhl K, Reed R, Hurt E (2002) TREEX is a conserved complex coupling transcription with messenger RNA export. Nature 417:304–307CrossRefPubMedGoogle Scholar
  48. Sudol M, Chen HI, Bougeret C, Einbond A, Bork P (1995) Characterization of a novel protein-binding module—the WW domain. FEBS Lett 369:67–71CrossRefPubMedGoogle Scholar
  49. Sun X, Alzhanova-Ericsson AT, Visa N, Aissouni Y, Zhao J, Daneholt B (1998) The hrp23 protein in the Balbiani ring pre-mRNA particles is released just before or at the binding the particles to the nuclear pore complex. J Cell Biol 142:1181–1193CrossRefPubMedGoogle Scholar
  50. Sune C, Garcia-Blanco MA (1999) Transcriptional cofactor CA150 regulates RNA polymerase II elongation in a TATA-box-dependent manner. Mol Cell Biol 19:4719–4728PubMedGoogle Scholar
  51. Sune C, Hayashi T, Liu Y, Lane W, Young RA, Garcia-Blanco MA (1997) CA150, a nuclear protein associated with RNA polymerase II holoenzyme, is involved in Tat-activated human immunodeficiency virus type 1 transcription. Mol Cell Biol 17:6029–6039PubMedGoogle Scholar
  52. Visa N, Alzhanova-Ericsson AT, Sun X, Kiseleva E, Björkroth B, Wurtz T, Daneholt B (1996) A pre-mRNA-binding protein accompanies the RNA from the gene through the nuclear pores and into polysomes. Cell 84:253–264CrossRefPubMedGoogle Scholar
  53. Wetterberg I, Baurén G, Wieslander L (1996) The intranuclear site of excision of each intron in Balbiani ring 3 pre-mRNA is influenced by the time remaining to transcription termination and different excision efficiencies for the various introns. RNA 2:641–651PubMedGoogle Scholar
  54. Wetterberg I, Zhao J, Masich S, Wieslander L, Skoglund U (2001) In situ transcription and splicing in the Balbiani ring 3 gene. EMBO J 20:2564–2574CrossRefPubMedGoogle Scholar
  55. Wieslander L (1994) The Balbiani ring multigene family: coding repetitive sequences and evolution of a tissue-specific cell function. Prog Nucleic Acid Res Mol Biol 48:275–313PubMedGoogle Scholar
  56. Wurtz T, Kiseleva E, Nacheva G, Alzhanova-Ericsson AT, Rosén, A, Daneholt B (1996) Identification of two RNA-binding proteins in Balbiani ring premessenger ribonucleoprotein granules and presence of these proteins in specific subsets of heterogeneous nuclear ribonucleoprotein particles. Mol Cell Biol 16:1425–1435PubMedGoogle Scholar
  57. Wyss C (1982) Ecdysterone, insulin and fly extract needed for the proliferation of normal Drosophila cells in defined medium. Exp Cell Res 139:297–307PubMedGoogle Scholar
  58. Zarrinpar A, Lim WA (2000) Converging on proline: the mechanism of WW domain peptide recognition. Nat Struct Biol 7:611–613CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Xin Sun
    • 1
  • Jian Zhao
    • 1
  • Karin Kylberg
    • 1
  • Teresa Soop
    • 1
  • Kevin Palka
    • 1
  • Erik Sonnhammer
    • 2
  • Neus Visa
    • 1
    • 3
  • Alla T. Alzhanova-Ericsson
    • 1
  • Bertil Daneholt
    • 1
  1. 1.Department of Cell and Molecular Biology, Medical Nobel InstituteKarolinska InstitutetStockholmSweden
  2. 2.Center for Genomics and BioinformaticsKarolinska InstitutetStockholmSweden
  3. 3.Department of Molecular Biology and Functional GenomicsStockholm UniversityStockholmSweden

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