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. 1997 Mar 17;16(6):1401–1412. doi: 10.1093/emboj/16.6.1401

Dynamic relocation of transcription and splicing factors dependent upon transcriptional activity.

C Zeng 1, E Kim 1, S L Warren 1, S M Berget 1
PMCID: PMC1169737  PMID: 9135155

Abstract

Recent interest in understanding the spatial organization of gene expression has focused attention on nuclear structures known as speckles or interchromatin granule clusters (IGCs) revealed by immunofluorescence or electron microscopy. Staining of nuclear factors involved in pre-mRNA splicing or, more recently, transcription, reveals 20-40 speckles per nucleus, resulting in the intriguing suggestion that speckles are nuclear sites of transcription and processing. In contrast, other investigations have observed transcription in other areas of the nucleus. In this study, we have examined the localization of active transcription as detected by uridine incorporation and recently developed RNA polymerase II antibodies, and compared this pattern with that of known splicing and polyadenylation factors. Our results indicate that in actively transcribing cells, transcription and splicing factors are dispersed throughout the nucleus with abundant sites of preferred localization. In contrast, in poorly transcribing cells, polymerase II and splicing factors localize to speckles. In nuclei inactivated for transcription by drugs or heat shock, the speckle type of co-localization is accentuated. These observations suggest that bulk transcription and splicing occur throughout the nucleus during periods of active transcription; and that factors involved in these two processes re-locate to minimal speckle domains during periods of inactive transcription.

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Selected References

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  1. Bartholomew B., Dahmus M. E., Meares C. F. RNA contacts subunits IIo and IIc in HeLa RNA polymerase II transcription complexes. J Biol Chem. 1986 Oct 25;261(30):14226–14231. [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. Bregman D. B., Du L., van der Zee S., Warren S. L. Transcription-dependent redistribution of the large subunit of RNA polymerase II to discrete nuclear domains. J Cell Biol. 1995 Apr;129(2):287–298. doi: 10.1083/jcb.129.2.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Carmo-Fonseca M., Pepperkok R., Carvalho M. T., Lamond A. I. Transcription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies. J Cell Biol. 1992 Apr;117(1):1–14. doi: 10.1083/jcb.117.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carmo-Fonseca M., Pepperkok R., Sproat B. S., Ansorge W., Swanson M. S., Lamond A. I. In vivo detection of snRNP-rich organelles in the nuclei of mammalian cells. EMBO J. 1991 Jul;10(7):1863–1873. doi: 10.1002/j.1460-2075.1991.tb07712.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Carmo-Fonseca M., Tollervey D., Pepperkok R., Barabino S. M., Merdes A., Brunner C., Zamore P. D., Green M. R., Hurt E., Lamond A. I. Mammalian nuclei contain foci which are highly enriched in components of the pre-mRNA splicing machinery. EMBO J. 1991 Jan;10(1):195–206. doi: 10.1002/j.1460-2075.1991.tb07936.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Carter K. C., Bowman D., Carrington W., Fogarty K., McNeil J. A., Fay F. S., Lawrence J. B. A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus. Science. 1993 Feb 26;259(5099):1330–1335. doi: 10.1126/science.8446902. [DOI] [PubMed] [Google Scholar]
  8. Carter K. C., Taneja K. L., Lawrence J. B. Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus. J Cell Biol. 1991 Dec;115(5):1191–1202. doi: 10.1083/jcb.115.5.1191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fakan S. Perichromatin fibrils are in situ forms of nascent transcripts. Trends Cell Biol. 1994 Mar;4(3):86–90. doi: 10.1016/0962-8924(94)90180-5. [DOI] [PubMed] [Google Scholar]
  10. Fakan S., Puvion E. The ultrastructural visualization of nucleolar and extranucleolar RNA synthesis and distribution. Int Rev Cytol. 1980;65:255–299. doi: 10.1016/s0074-7696(08)61962-2. [DOI] [PubMed] [Google Scholar]
  11. Fey E. G., Krochmalnic G., Penman S. The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy. J Cell Biol. 1986 May;102(5):1654–1665. doi: 10.1083/jcb.102.5.1654. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Harpold M. M., Wilson M. C., Darnell J. E., Jr Chinese hamster polyadenylated messenger ribonucleic acid: relationship to non-polyadenylated sequences and relative conservation during messenger ribonucleic acid processing. Mol Cell Biol. 1981 Feb;1(2):188–198. doi: 10.1128/mcb.1.2.188. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hendzel M. J., Bazett-Jones D. P. RNA polymerase II transcription and the functional organization of the mammalian cell nucleus. Chromosoma. 1995 Feb;103(8):509–516. doi: 10.1007/BF00355315. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Huang S., Spector D. L. Nascent pre-mRNA transcripts are associated with nuclear regions enriched in splicing factors. Genes Dev. 1991 Dec;5(12A):2288–2302. doi: 10.1101/gad.5.12a.2288. [DOI] [PubMed] [Google Scholar]
  16. Huang S., Spector D. L. U1 and U2 small nuclear RNAs are present in nuclear speckles. Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):305–308. doi: 10.1073/pnas.89.1.305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Jenny A., Hauri H. P., Keller W. Characterization of cleavage and polyadenylation specificity factor and cloning of its 100-kilodalton subunit. Mol Cell Biol. 1994 Dec;14(12):8183–8190. doi: 10.1128/mcb.14.12.8183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Krause S., Fakan S., Weis K., Wahle E. Immunodetection of poly(A) binding protein II in the cell nucleus. Exp Cell Res. 1994 Sep;214(1):75–82. doi: 10.1006/excr.1994.1235. [DOI] [PubMed] [Google Scholar]
  19. Lawrence J. B., Carter K. C., Xing X. Probing functional organization within the nucleus: is genome structure integrated with RNA metabolism? Cold Spring Harb Symp Quant Biol. 1993;58:807–818. doi: 10.1101/sqb.1993.058.01.088. [DOI] [PubMed] [Google Scholar]
  20. Laybourn P. J., Dahmus M. E. Phosphorylation of RNA polymerase IIA occurs subsequent to interaction with the promoter and before the initiation of transcription. J Biol Chem. 1990 Aug 5;265(22):13165–13173. [PubMed] [Google Scholar]
  21. Möbus V., Gerharz C. D., Press U., Moll R., Beck T., Mellin W., Pollow K., Knapstein P. G., Kreienberg R. Morphological, immunohistochemical and biochemical characterization of 6 newly established human ovarian carcinoma cell lines. Int J Cancer. 1992 Aug 19;52(1):76–84. doi: 10.1002/ijc.2910520115. [DOI] [PubMed] [Google Scholar]
  22. Nyman U., Hallman H., Hadlaczky G., Pettersson I., Sharp G., Ringertz N. R. Intranuclear localization of snRNP antigens. J Cell Biol. 1986 Jan;102(1):137–144. doi: 10.1083/jcb.102.1.137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Salditt-Georgieff M., Harpold M. M., Wilson M. C., Darnell J. E., Jr Large heterogeneous nuclear ribonucleic acid has three times as many 5' caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol Cell Biol. 1981 Feb;1(2):179–187. doi: 10.1128/mcb.1.2.179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Spector D. L., Fu X. D., Maniatis T. Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 1991 Nov;10(11):3467–3481. doi: 10.1002/j.1460-2075.1991.tb04911.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. 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]
  26. Takagaki Y., Manley J. L., MacDonald C. C., Wilusz J., Shenk T. A multisubunit factor, CstF, is required for polyadenylation of mammalian pre-mRNAs. Genes Dev. 1990 Dec;4(12A):2112–2120. doi: 10.1101/gad.4.12a.2112. [DOI] [PubMed] [Google Scholar]
  27. Wang J., Cao L. G., Wang Y. L., Pederson T. Localization of pre-messenger RNA at discrete nuclear sites. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7391–7395. doi: 10.1073/pnas.88.16.7391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wansink D. G., Nelissen R. L., de Jong L. In vitro splicing of pre-mRNA containing bromouridine. Mol Biol Rep. 1994 Mar;19(2):109–113. doi: 10.1007/BF00997156. [DOI] [PubMed] [Google Scholar]
  29. Wansink D. G., Schul W., van der Kraan I., van Steensel B., van Driel R., de Jong L. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J Cell Biol. 1993 Jul;122(2):283–293. doi: 10.1083/jcb.122.2.283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Xing Y., Johnson C. V., Dobner P. R., Lawrence J. B. Higher level organization of individual gene transcription and RNA splicing. Science. 1993 Feb 26;259(5099):1326–1330. doi: 10.1126/science.8446901. [DOI] [PubMed] [Google Scholar]
  31. Yuryev A., Patturajan M., Litingtung Y., Joshi R. V., Gentile C., Gebara M., Corden J. L. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):6975–6980. doi: 10.1073/pnas.93.14.6975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Zahler A. M., Lane W. S., Stolk J. A., Roth M. B. SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev. 1992 May;6(5):837–847. doi: 10.1101/gad.6.5.837. [DOI] [PubMed] [Google Scholar]

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