Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2015 (2015), Article ID 395816, 9 pages
http://dx.doi.org/10.1155/2015/395816
Research Article

Unravelling the RNA-Binding Properties of SAFB Proteins in Breast Cancer Cells

1Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
2Institute of Genetic Medicine, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
3Faculty of Computer and Information Science, University of Ljubljana, Traska Cesta 25, 51-1000 Ljubljana, Slovenia

Received 29 January 2015; Accepted 15 April 2015

Academic Editor: Claudia Ghigna

Copyright © 2015 Elaine Hong et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. O. Nayler, W. Strätling, J.-P. Bourquin et al., “SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements,” Nucleic Acids Research, vol. 26, no. 15, pp. 3542–3549, 1998. View at Publisher · View at Google Scholar · View at Scopus
  2. Y. Arao, R. Kuriyama, F. Kayama, and S. Kato, “A nuclear matrix-associated factor, SAFB-B, interacts with specific isoforms of AUF1/hnRNP D,” Archives of Biochemistry and Biophysics, vol. 380, no. 2, pp. 228–236, 2000. View at Publisher · View at Google Scholar · View at Scopus
  3. E. Nikolakaki, R. Kohen, A. M. Hartmann, S. Stamm, E. Georgatsou, and T. Giannakouros, “Cloning and characterization of an alternatively spliced form of SR protein kinase 1 that interacts specifically with scaffold attachment factor-B,” The Journal of Biological Chemistry, vol. 276, no. 43, pp. 40175–40182, 2001. View at Publisher · View at Google Scholar · View at Scopus
  4. J. Li, I. C. Hawkins, C. D. Harvey, J. L. Jennings, A. J. Link, and J. G. Patton, “Regulation of alternative splicing by SRrp86 and its interacting proteins,” Molecular and Cellular Biology, vol. 23, no. 21, pp. 7437–7447, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. K. A. Sergeant, C. F. Bourgeois, C. Dalgliesh, J. P. Venables, J. Stevenin, and D. J. Elliott, “Alternative RNA splicing complexes containing the scaffold attachment factor SAFB2,” Journal of Cell Science, vol. 120, no. 2, pp. 309–319, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. F. Weighardt, F. Cobianchi, L. Cartegni et al., “A novel hnRNP protein (HAP/SAF-B) enters a subset of hnRNP complexes and relocates in nuclear granules in response to heat shock,” Journal of Cell Science, vol. 112, no. 10, pp. 1465–1476, 1999. View at Google Scholar · View at Scopus
  7. P. Stoilov, R. Dauod, O. Nayler, and S. Stamm, “Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA,” Human Molecular Genetics, vol. 13, no. 5, pp. 509–524, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. S. M. Townson, K. Kang, A. V. Lee, and S. Oesterreich, “Structure-function analysis of the estrogen receptor α corepressor scaffold attachment factor-B1: identification of a potent transcriptional repression domain,” The Journal of Biological Chemistry, vol. 279, no. 25, pp. 26074–26081, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. J. Konig, K. Zarnack, G. Rot et al., “iCLIP—transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution,” The Journal of Visualized Experiments, no. 50, Article ID e2638, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. F. Acconcia, P. Ascenzi, A. Bocedi et al., “Palmitoylation-dependent estrogen receptor alpha membrane localization: regulation by 17beta-estradiol,” Molecular Biology of the Cell, vol. 16, no. 1, pp. 231–237, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. J. König, K. Zarnack, G. Rot et al., “ICLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution,” Nature Structural and Molecular Biology, vol. 17, no. 7, pp. 909–915, 2010. View at Publisher · View at Google Scholar · View at Scopus
  12. J. Ule, K. B. Jensen, M. Ruggiu, A. Mele, A. Ule, and R. B. Darnell, “CLIP identifies Nova-regulated RNA networks in the brain,” Science, vol. 302, no. 5648, pp. 1212–1215, 2003. View at Publisher · View at Google Scholar · View at Scopus
  13. Z. Wang, M. Kayikci, M. Briese et al., “iCLIP predicts the dual splicing effects of TIA-RNA interactions,” PLoS Biology, vol. 8, no. 10, Article ID e1000530, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. T. A. Y. Ayoubi and W. J. M. van de Ven, “Regulation of gene expression by alternative promoters,” The FASEB Journal, vol. 10, no. 4, pp. 453–460, 1996. View at Google Scholar · View at Scopus
  15. R. V. Davuluri, Y. Suzuki, S. Sugano, C. Plass, and T. H.-M. Huang, “The functional consequences of alternative promoter use in mammalian genomes,” Trends in Genetics, vol. 24, no. 4, pp. 167–177, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. F. Koch, F. Jourquin, P. Ferrier, and J.-C. Andrau, “Genome-wide RNA polymerase II: not genes only!,” Trends in Biochemical Sciences, vol. 33, no. 6, pp. 265–273, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. G. A. C. Singer, J. Wu, P. Yan, C. Plass, T. H. M. Huang, and R. V. Davuluri, “Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array,” BMC Genomics, vol. 9, article 349, 2008. View at Publisher · View at Google Scholar · View at Scopus
  18. V. Tripathi, J. D. Ellis, Z. Shen et al., “The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation,” Molecular Cell, vol. 39, no. 6, pp. 925–938, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. L. Li, T. Feng, Y. Lian, G. Zhang, A. Garen, and X. Song, “Role of human noncoding RNAs in the control of tumorigenesis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 31, pp. 12956–12961, 2009. View at Publisher · View at Google Scholar · View at Scopus
  20. D. S. Perez, T. R. Hoage, J. R. Pritchett et al., “Long, abundantly expressed non-coding transcripts are altered in cancer,” Human Molecular Genetics, vol. 17, no. 5, pp. 642–655, 2008. View at Publisher · View at Google Scholar · View at Scopus
  21. M.-L. Änkö, M. Müller-McNicoll, H. Brandl et al., “The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes,” Genome Biology, vol. 13, no. 3, article R17, 2012. View at Publisher · View at Google Scholar · View at Scopus
  22. J. S. Mattick and I. V. Makunin, “Non-coding RNA,” Human Molecular Genetics, vol. 15, no. 1, pp. R17–R29, 2006. View at Publisher · View at Google Scholar · View at Scopus
  23. H. Busch, R. Reddy, L. Rothblum, and Y. C. Choi, “SnRNAs, SnRNPs, and RNA processing,” Annual Review of Biochemistry, vol. 51, pp. 617–654, 1982. View at Publisher · View at Google Scholar · View at Scopus
  24. M. C. Wahl, C. L. Will, and R. Lührmann, “The spliceosome: design principles of a dynamic RNP machine,” Cell, vol. 136, no. 4, pp. 701–718, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. J. Rappsilber, U. Ryder, A. I. Lamond, and M. Mann, “Large-scale proteomic analysis of the human spliceosome,” Genome Research, vol. 12, no. 8, pp. 1231–1245, 2002. View at Publisher · View at Google Scholar · View at Scopus
  26. J. C. Long and J. F. Caceres, “The SR protein family of splicing factors: master regulators of gene expression,” Biochemical Journal, vol. 417, no. 1, pp. 15–27, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. C. K. Lindholm, J. D. Frantz, S. E. Shoelson, and M. Welsh, “Shf, a Shb-like adapter protein, is involved in PDGF-α-receptor regulation of apoptosis,” Biochemical and Biophysical Research Communications, vol. 278, no. 3, pp. 537–543, 2000. View at Publisher · View at Google Scholar · View at Scopus
  28. M. Welsh, J. Mares, T. Karlsson, C. Lavergne, B. Breant, and L. Claesson-Welsh, “Shb is a ubiquitously expressed Src homology 2 protein,” Oncogene, vol. 9, no. 1, pp. 19–27, 1994. View at Google Scholar · View at Scopus
  29. M. Ohira, A. Morohashi, H. Inuzuka et al., “Expression profiling and characterization of 4200 genes cloned from primary neuroblastomas: identification of 305 genes differentially expressed between favorable and unfavorable subsets,” Oncogene, vol. 22, no. 35, pp. 5525–5536, 2003. View at Publisher · View at Google Scholar · View at Scopus
  30. D. Takagi, Y. Tatsumi, T. Yokochi et al., “Novel adaptor protein Shf interacts with ALK receptor and negatively regulates its downstream signals in neuroblastoma,” Cancer Science, vol. 104, no. 5, pp. 563–572, 2013. View at Publisher · View at Google Scholar · View at Scopus
  31. A. S. Clarke, M. M. Lotz, and A. M. Mercurio, “A novel structural variant of the human β4 integrin cDNA,” Cell Adhesion and Communication, vol. 2, no. 1, pp. 1–6, 1994. View at Publisher · View at Google Scholar · View at Scopus
  32. R. N. Tamura, C. Rozzo, L. Starr et al., “Epithelial integrin α6β4: complete primary structure of α6 and variant forms of β4,” Journal of Cell Biology, vol. 111, no. 4, pp. 1593–1604, 1990. View at Publisher · View at Google Scholar · View at Scopus
  33. M. R. van Leusden, I. Kuikman, and A. Sonnenberg, “The unique cytoplasmic domain of the human integrin variant β4E is produced by partial retention of intronic sequences,” Biochemical and Biophysical Research Communications, vol. 235, no. 3, pp. 826–830, 1997. View at Publisher · View at Google Scholar · View at Scopus
  34. A. A. de Melker and A. Sonnenberg, “Integrins: alternative splicing as a mechanism to regulate ligand binding and integrin signaling events,” BioEssays, vol. 21, no. 6, pp. 499–509, 1999. View at Google Scholar · View at Scopus
  35. J. N. Hutchinson, A. W. Ensminger, C. M. Clemson, C. R. Lynch, J. B. Lawrence, and A. Chess, “A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains,” BMC Genomics, vol. 8, article 39, 2007. View at Publisher · View at Google Scholar · View at Scopus
  36. J. R. Sanford, X. Wang, M. Mort et al., “Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts,” Genome Research, vol. 19, no. 3, pp. 381–394, 2009. View at Publisher · View at Google Scholar · View at Scopus
  37. S. Hammerich-Hille, B. A. Kaipparettu, A. Tsimelzon et al., “SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells,” The Journal of Biological Chemistry, vol. 285, no. 6, pp. 3608–3616, 2010. View at Publisher · View at Google Scholar · View at Scopus
  38. M. Ivanova, K. M. Dobrzycka, S. Jiang et al., “Scaffold attachment factor B1 functions in development, growth, and reproduction,” Molecular and Cellular Biology, vol. 25, no. 8, pp. 2995–3006, 2005. View at Publisher · View at Google Scholar · View at Scopus