RNA Pol II transcription sites show a significant but incomplete colocalisation with RNA pol II (marked by the incorporation of Br-UTP into nascent RNA) and occur as discrete foci in the nucleoplasm (Iborra, F. J., et al. 1996). These foci vary in size from 40-80nm. Likewise, RNA Pol III is found to localise to dedicated nucleoplasmic transcription sites of similar size (Grande M. A., et al. 1997) . The number of transcription sites ranges from 500-10,000 per cell, but RNA Pol II also localises to numerous domains outside these transcription sites (Pombo, A., et al. 1999) .

In HeLa cells, there is estimated to be 5000 to 8000 RNA Pol II sites and ~2000 RNA Pol III sites. Since there are approximately 20,000 to 100,000 active

polymerases per mammalian cell nucleus and since typically, HeLa cells contain ~90,000 nascent transcripts (15,000 made by polymerase I and ~75,000 by polymerase II and III, it follows that most nascent RNA transcripts associate with only one polymerase and this was found to be the case (Jackson, D. A., et al. 1998).

The Concept of Transcription Factories

As the number of pol II transcription sites has always been estimated to be less than the number of active polymerases, one would expect that each site might be associated with more than one transcription unit, estimated at ~30 such units per site in HeLa cells (Jackson, D. A., et al. 1998) . Hence these sites are termed "transcription factories". The transcription factor TFIIH significantly co-distributes with RNA Pol II and transcription factories in immunolabelling experiments (Grande M. A., et al. 1997) , whereas many other transcription factors have been found to be in domains spatially distinct from these, possibly representing storage storage sites or incomplete transcription initiation complexes. Therefore, the transcription factory can be seen as a tripartate structure containing mainly spatially contiguous template, RNA polymerase II and newly synthesised mRNA.

To rationalise both the size (80 nm) and the tripartate structure of the transcription factory, one model suggests that the polymerase is fixed by attachment to the transcription site rather than being able to track along template. New transcripts are extruded into the site and the "cloud" of transcription units would surround it. The template would move along the RNA Polymerase and rotate rather than the polymerase tracking along the template and rotating. This model is consistent with the fact that still-engaged polymerases and transcribed DNA remains even after nuclease treatment (Jackson, D. A., et al. 1996) , suggesting that the polymerase is attached to some underlying substructure in the nucleoplasm. A review by Cook (1999; and references within) gives evidence for and against this model .

Transcription Factories as Multifunctional Supercomplexes

Although transcription sites are spatially distinct from sites of replication (Wei, X., et al. 1998) , RNA Pol II factories are implicated in other cellular events including the processing and translation of RNA. Recent evidence suggests that RNA pol II can associate with other factors to form large multifunctional holoenzymes, which can cap, polyadenylate and splice mRNA (Myers, V. E., et al. 1998) . Some translation also appears to be coupled with transcription at transcription factories in Hela nuclei. This transcription-coupled translation may occur in the nucleus as part of the non-sense mediated decay of aberrant RNA transcripts. (Iborra, F. J., et al. 2001).

Other Internet Resources on SNBs

  • Ana Pombo's Home Page--Images of Transcription factories and an overview of Dr. Pombo's research.

  • Peter Cook's Home Page--Images of Nucleis and overview of Dr. Cook's research

  • Pavel Hozak's Web Site--Info on transcription and replication factories as well as translation in the nucleus


    Cook PR (1999) The organization of replication and transcription. Science. 284(5421):1790-1795

    Grande MA, van der Kraan I, de Jong L, van Driel R. (1997) Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci.110 (15):1781-1791.

    Iborra FJ, Pombo A, Jackson DA, Cook PR.(1996) Active RNA polymerases are localized within discrete transcription "factories' in human nuclei. J. Cell Sci. 109 (6):1427-1436

    Iborra FJ, Jackson DA, Cook PR.(2001) Coupled transcription and translation within nuclei of mammalian cells Science. 2001 293(5532):1139-1142.

    Jackson DA, Bartlett J, Cook PR.(1996) Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: the role of transcription units. Nucl. Acids Res. 24(7):1212-1219

    Jackson DA, Iborra FJ, Manders EM, Cook PR. (1998) Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol Biol Cell. 9(6):1523-1536.

    Myer VE, Young RA (1998) RNA polymerase II holoenzymes and subcomplexes. J. Biol Chem. 273(43):27757-22760

    Pombo A, Jackson DA, Hollinshead M, Wang Z, Roeder RG, Cook PR.(1999) Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18(8):2241-2253.

    Wei X, Samarabandu J, Devdhar RS, Siegel AJ, Acharya R. and Berezney R (1998) Segregation of transcription and replication sites into higher order domains. Science. 281(5382):1502-1506