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. 1998 Aug 1;26(15):3542–3549. doi: 10.1093/nar/26.15.3542

SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements.

O Nayler 1, W Strätling 1, J P Bourquin 1, I Stagljar 1, L Lindemann 1, H Jasper 1, A M Hartmann 1, F O Fackelmayer 1, A Ullrich 1, S Stamm 1
PMCID: PMC147731  PMID: 9671816

Abstract

Interphase chromatin is arranged into topologically separated domains comprising gene expression and replication units through genomic sequence elements, so-called MAR or SAR regions (for matrix- or scaffold-associating regions). S/MAR regions are located near the boundaries of actively transcribed genes and were shown to influence their activity. We show that scaffold attachment factor B (SAF-B), which specifically binds to S/MAR regions, interacts with RNA polymerase II (RNA pol II) and a subset of serine-/arginine-rich RNA processing factors (SR proteins). SAF-B localized to the nucleus in a speckled pattern that coincided with the distribution of the SR protein SC35. Furthermore, we show that overexpressed SAF-B induced an increase of the 10S splice product using an E1A reporter gene and repressed the activity of an S/MAR flanked CAT reporter gene construct in vivo . This indicates an association of SAF-B with SR proteins and components of the transcription machinery. Our results describe the coupling of a chromatin organizing S/MAR element with transcription and pre-mRNA processing components and we propose that SAF-B serves as a molecular base to assemble a 'transcriptosome complex' in the vicinity of actively transcribed genes.

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Selected References

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  1. Beil B., Screaton G., Stamm S. Molecular cloning of htra2-beta-1 and htra2-beta-2, two human homologs of tra-2 generated by alternative splicing. DNA Cell Biol. 1997 Jun;16(6):679–690. doi: 10.1089/dna.1997.16.679. [DOI] [PubMed] [Google Scholar]
  2. Beyer A. L., Osheim Y. N. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev. 1988 Jun;2(6):754–765. doi: 10.1101/gad.2.6.754. [DOI] [PubMed] [Google Scholar]
  3. Blencowe B. J., Nickerson J. A., Issner R., Penman S., Sharp P. A. Association of nuclear matrix antigens with exon-containing splicing complexes. J Cell Biol. 1994 Nov;127(3):593–607. doi: 10.1083/jcb.127.3.593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bode J., Kohwi Y., Dickinson L., Joh T., Klehr D., Mielke C., Kohwi-Shigematsu T. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science. 1992 Jan 10;255(5041):195–197. doi: 10.1126/science.1553545. [DOI] [PubMed] [Google Scholar]
  5. Boulikas T. Chromatin domains and prediction of MAR sequences. Int Rev Cytol. 1995;162A:279–388. doi: 10.1016/s0074-7696(08)61234-6. [DOI] [PubMed] [Google Scholar]
  6. Bourquin J. P., Stagljar I., Meier P., Moosmann P., Silke J., Baechi T., Georgiev O., Schaffner W. A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. Nucleic Acids Res. 1997 Jun 1;25(11):2055–2061. doi: 10.1093/nar/25.11.2055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cairns B. R. Chromatin remodeling machines: similar motors, ulterior motives. Trends Biochem Sci. 1998 Jan;23(1):20–25. doi: 10.1016/s0968-0004(97)01160-2. [DOI] [PubMed] [Google Scholar]
  8. Colwill K., Pawson T., Andrews B., Prasad J., Manley J. L., Bell J. C., Duncan P. I. The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J. 1996 Jan 15;15(2):265–275. [PMC free article] [PubMed] [Google Scholar]
  9. Corden J. L., Patturajan M. A CTD function linking transcription to splicing. Trends Biochem Sci. 1997 Nov;22(11):413–416. doi: 10.1016/s0968-0004(97)01125-0. [DOI] [PubMed] [Google Scholar]
  10. Cáceres J. F., Stamm S., Helfman D. M., Krainer A. R. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science. 1994 Sep 16;265(5179):1706–1709. doi: 10.1126/science.8085156. [DOI] [PubMed] [Google Scholar]
  11. Dickinson L. A., Joh T., Kohwi Y., Kohwi-Shigematsu T. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell. 1992 Aug 21;70(4):631–645. doi: 10.1016/0092-8674(92)90432-c. [DOI] [PubMed] [Google Scholar]
  12. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Du L., Warren S. L. A functional interaction between the carboxy-terminal domain of RNA polymerase II and pre-mRNA splicing. J Cell Biol. 1997 Jan 13;136(1):5–18. doi: 10.1083/jcb.136.1.5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Forrester W. C., van Genderen C., Jenuwein T., Grosschedl R. Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions. Science. 1994 Aug 26;265(5176):1221–1225. doi: 10.1126/science.8066460. [DOI] [PubMed] [Google Scholar]
  15. Fu X. D., Maniatis T. Isolation of a complementary DNA that encodes the mammalian splicing factor SC35. Science. 1992 Apr 24;256(5056):535–538. doi: 10.1126/science.1373910. [DOI] [PubMed] [Google Scholar]
  16. Fu X. D. The superfamily of arginine/serine-rich splicing factors. RNA. 1995 Sep;1(7):663–680. [PMC free article] [PubMed] [Google Scholar]
  17. Ge H., Manley J. L. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell. 1990 Jul 13;62(1):25–34. doi: 10.1016/0092-8674(90)90236-8. [DOI] [PubMed] [Google Scholar]
  18. Ge H., Zuo P., Manley J. L. Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators. Cell. 1991 Jul 26;66(2):373–382. doi: 10.1016/0092-8674(91)90626-a. [DOI] [PubMed] [Google Scholar]
  19. Geertman R., McMahon A., Sabban E. L. Cloning and characterization of cDNAs for novel proteins with glutamic acid-proline dipeptide tandem repeats. Biochim Biophys Acta. 1996 May 2;1306(2-3):147–152. doi: 10.1016/0167-4781(96)00036-x. [DOI] [PubMed] [Google Scholar]
  20. Görlich D., Mattaj I. W. Nucleocytoplasmic transport. Science. 1996 Mar 15;271(5255):1513–1518. doi: 10.1126/science.271.5255.1513. [DOI] [PubMed] [Google Scholar]
  21. Huang S., Spector D. L. Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J Cell Biol. 1996 May;133(4):719–732. doi: 10.1083/jcb.133.4.719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hörtnagel K., Mautner J., Strobl L. J., Wolf D. A., Christoph B., Geltinger C., Polack A. The role of immunoglobulin kappa elements in c-myc activation. Oncogene. 1995 Apr 6;10(7):1393–1401. [PubMed] [Google Scholar]
  23. Jeppesen P. Histone acetylation: a possible mechanism for the inheritance of cell memory at mitosis. Bioessays. 1997 Jan;19(1):67–74. doi: 10.1002/bies.950190111. [DOI] [PubMed] [Google Scholar]
  24. Kim E., Du L., Bregman D. B., Warren S. L. Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA. J Cell Biol. 1997 Jan 13;136(1):19–28. doi: 10.1083/jcb.136.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kohwi-Shigematsu T., Maass K., Bode J. A thymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes. Biochemistry. 1997 Oct 7;36(40):12005–12010. doi: 10.1021/bi971444j. [DOI] [PubMed] [Google Scholar]
  26. Krämer A. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem. 1996;65:367–409. doi: 10.1146/annurev.bi.65.070196.002055. [DOI] [PubMed] [Google Scholar]
  27. Liu J., Bramblett D., Zhu Q., Lozano M., Kobayashi R., Ross S. R., Dudley J. P. The matrix attachment region-binding protein SATB1 participates in negative regulation of tissue-specific gene expression. Mol Cell Biol. 1997 Sep;17(9):5275–5287. doi: 10.1128/mcb.17.9.5275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Manley J. L., Tacke R. SR proteins and splicing control. Genes Dev. 1996 Jul 1;10(13):1569–1579. doi: 10.1101/gad.10.13.1569. [DOI] [PubMed] [Google Scholar]
  29. Mayeda A., Krainer A. R. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell. 1992 Jan 24;68(2):365–375. doi: 10.1016/0092-8674(92)90477-t. [DOI] [PubMed] [Google Scholar]
  30. McCracken S., Fong N., Yankulov K., Ballantyne S., Pan G., Greenblatt J., Patterson S. D., Wickens M., Bentley D. L. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature. 1997 Jan 23;385(6614):357–361. doi: 10.1038/385357a0. [DOI] [PubMed] [Google Scholar]
  31. Misteli T., Cáceres J. F., Spector D. L. The dynamics of a pre-mRNA splicing factor in living cells. Nature. 1997 May 29;387(6632):523–527. doi: 10.1038/387523a0. [DOI] [PubMed] [Google Scholar]
  32. Namciu S. J., Blochlinger K. B., Fournier R. E. Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster. Mol Cell Biol. 1998 Apr;18(4):2382–2391. doi: 10.1128/mcb.18.4.2382. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Nan X., Campoy F. J., Bird A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell. 1997 Feb 21;88(4):471–481. doi: 10.1016/s0092-8674(00)81887-5. [DOI] [PubMed] [Google Scholar]
  34. Narayan P., Rottman F. M. Methylation of mRNA. Adv Enzymol Relat Areas Mol Biol. 1992;65:255–285. doi: 10.1002/9780470123119.ch7. [DOI] [PubMed] [Google Scholar]
  35. Nayler O., Stamm S., Ullrich A. Characterization and comparison of four serine- and arginine-rich (SR) protein kinases. Biochem J. 1997 Sep 15;326(Pt 3):693–700. doi: 10.1042/bj3260693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Neugebauer K. M., Roth M. B. Transcription units as RNA processing units. Genes Dev. 1997 Dec 15;11(24):3279–3285. doi: 10.1101/gad.11.24.3279. [DOI] [PubMed] [Google Scholar]
  37. Nickerson J. A., Blencowe B. J., Penman S. The architectural organization of nuclear metabolism. Int Rev Cytol. 1995;162A:67–123. doi: 10.1016/s0074-7696(08)61229-2. [DOI] [PubMed] [Google Scholar]
  38. Oesterreich S., Lee A. V., Sullivan T. M., Samuel S. K., Davie J. R., Fuqua S. A. Novel nuclear matrix protein HET binds to and influences activity of the HSP27 promoter in human breast cancer cells. J Cell Biochem. 1997 Nov 1;67(2):275–286. [PubMed] [Google Scholar]
  39. Phi-Van L., Strätling W. H. Dissection of the ability of the chicken lysozyme gene 5' matrix attachment region to stimulate transgene expression and to dampen position effects. Biochemistry. 1996 Aug 20;35(33):10735–10742. doi: 10.1021/bi9603783. [DOI] [PubMed] [Google Scholar]
  40. Ptashne M., Gann A. Transcriptional activation by recruitment. Nature. 1997 Apr 10;386(6625):569–577. doi: 10.1038/386569a0. [DOI] [PubMed] [Google Scholar]
  41. Raska I. Nuclear ultrastructures associated with the RNA synthesis and processing. J Cell Biochem. 1995 Sep;59(1):11–26. doi: 10.1002/jcb.240590103. [DOI] [PubMed] [Google Scholar]
  42. Renz A., Fackelmayer F. O. Purification and molecular cloning of the scaffold attachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA. Nucleic Acids Res. 1996 Mar 1;24(5):843–849. doi: 10.1093/nar/24.5.843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Roth M. B., Murphy C., Gall J. G. A monoclonal antibody that recognizes a phosphorylated epitope stains lampbrush chromosome loops and small granules in the amphibian germinal vesicle. J Cell Biol. 1990 Dec;111(6 Pt 1):2217–2223. doi: 10.1083/jcb.111.6.2217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Ruiz-Echevarria M. J., Czaplinski K., Peltz S. W. Making sense of nonsense in yeast. Trends Biochem Sci. 1996 Nov;21(11):433–438. doi: 10.1016/s0968-0004(96)10055-4. [DOI] [PubMed] [Google Scholar]
  45. Sachs A. B. Messenger RNA degradation in eukaryotes. Cell. 1993 Aug 13;74(3):413–421. doi: 10.1016/0092-8674(93)80043-e. [DOI] [PubMed] [Google Scholar]
  46. Schmauss C., McAllister G., Ohosone Y., Hardin J. A., Lerner M. R. A comparison of snRNP-associated Sm-autoantigens: human N, rat N and human B/B'. Nucleic Acids Res. 1989 Feb 25;17(4):1733–1743. doi: 10.1093/nar/17.4.1733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Screaton G. R., Cáceres J. F., Mayeda A., Bell M. V., Plebanski M., Jackson D. G., Bell J. I., Krainer A. R. Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J. 1995 Sep 1;14(17):4336–4349. doi: 10.1002/j.1460-2075.1995.tb00108.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Siegfried Z., Cedar H. DNA methylation: a molecular lock. Curr Biol. 1997 May 1;7(5):R305–R307. doi: 10.1016/s0960-9822(06)00144-8. [DOI] [PubMed] [Google Scholar]
  49. Spector D. L. Macromolecular domains within the cell nucleus. Annu Rev Cell Biol. 1993;9:265–315. doi: 10.1146/annurev.cb.09.110193.001405. [DOI] [PubMed] [Google Scholar]
  50. Stief A., Winter D. M., Strätling W. H., Sippel A. E. A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature. 1989 Sep 28;341(6240):343–345. doi: 10.1038/341343a0. [DOI] [PubMed] [Google Scholar]
  51. Tate P. H., Bird A. P. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr Opin Genet Dev. 1993 Apr;3(2):226–231. doi: 10.1016/0959-437x(93)90027-m. [DOI] [PubMed] [Google Scholar]
  52. Wang J., Manley J. L. Overexpression of the SR proteins ASF/SF2 and SC35 influences alternative splicing in vivo in diverse ways. RNA. 1995 May;1(3):335–346. [PMC free article] [PubMed] [Google Scholar]
  53. Weitzel J. M., Buhrmester H., Strätling W. H. Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG-binding protein MeCP2. Mol Cell Biol. 1997 Sep;17(9):5656–5666. doi: 10.1128/mcb.17.9.5656. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Will C. L., Lührmann R. Protein functions in pre-mRNA splicing. Curr Opin Cell Biol. 1997 Jun;9(3):320–328. doi: 10.1016/s0955-0674(97)80003-8. [DOI] [PubMed] [Google Scholar]
  55. Xing Y., Johnson C. V., Moen P. T., Jr, McNeil J. A., Lawrence J. Nonrandom gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J Cell Biol. 1995 Dec;131(6 Pt 2):1635–1647. doi: 10.1083/jcb.131.6.1635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Zamore P. D., Patton J. G., Green M. R. Cloning and domain structure of the mammalian splicing factor U2AF. Nature. 1992 Feb 13;355(6361):609–614. doi: 10.1038/355609a0. [DOI] [PubMed] [Google Scholar]
  57. van Driel R., Wansink D. G., van Steensel B., Grande M. A., Schul W., de Jong L. Nuclear domains and the nuclear matrix. Int Rev Cytol. 1995;162A:151–189. doi: 10.1016/s0074-7696(08)61231-0. [DOI] [PubMed] [Google Scholar]
  58. van der Geer P., Hunter T. Phosphopeptide mapping and phosphoamino acid analysis by electrophoresis and chromatography on thin-layer cellulose plates. Electrophoresis. 1994 Mar-Apr;15(3-4):544–554. doi: 10.1002/elps.1150150173. [DOI] [PubMed] [Google Scholar]

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