Transcription Factories: Quantitative Studies of Nanostructures in the Mammalian Nucleus

Overview

Journal Chromosome Res

Date 2003 Sep 16

PMID 12971722

Citations 23

Authors

Sonya Martin

Ana Pombo

Affiliations

Soon will be listed here.

Abstract

Transcription by the three nuclear RNA polymerases is carried out in transcription factories. This conclusion has been drawn from estimates of the total number of nascent transcripts or active polymerase molecules and the number of transcription sites within a cell. Here we summarise the variety of methods used to determine these parameters, discuss their associated problems and outline future prospects.

Citing Articles

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References

WARREN S, Landolfi A, Curtis C, Morrow J . Cytostellin: a novel, highly conserved protein that undergoes continuous redistribution during the cell cycle. J Cell Sci. 1992; 103 ( Pt 2):381-8. DOI: 10.1242/jcs.103.2.381. View

Reimer G, Raska I, Tan E, Scheer U . Human autoantibodies: probes for nucleolus structure and function. Virchows Arch B Cell Pathol Incl Mol Pathol. 1987; 54(3):131-43. DOI: 10.1007/BF02899205. View

Wansink D, Nelissen R, de Jong L . In vitro splicing of pre-mRNA containing bromouridine. Mol Biol Rep. 1994; 19(2):109-13. DOI: 10.1007/BF00997156. View

Failla A, Spoeri U, Albrecht B, Kroll A, Cremer C . Nanosizing of fluorescent objects by spatially modulated illumination microscopy. Appl Opt. 2002; 41(34):7275-83. DOI: 10.1364/ao.41.007275. View

PUVION E . Ultrastructure of the nucleus in relation to transcription and splicing: roles of perichromatin fibrils and interchromatin granules. Exp Cell Res. 1996; 229(2):217-25. DOI: 10.1006/excr.1996.0363. View

Sadoni N, Sullivan K, Weinzierl P, Stelzer E, Zink D . Large-scale chromatin fibers of living cells display a discontinuous functional organization. Chromosoma. 2001; 110(1):39-51. DOI: 10.1007/s004120000123. View

Orphanides G, Reinberg D . A unified theory of gene expression. Cell. 2002; 108(4):439-51. DOI: 10.1016/s0092-8674(02)00655-4. View

Horn P, Peterson C . Molecular biology. Chromatin higher order folding--wrapping up transcription. Science. 2002; 297(5588):1824-7. DOI: 10.1126/science.1074200. View

Jackson D, Iborra F, Manders E, Cook P . Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol Biol Cell. 1998; 9(6):1523-36. PMC: 25378. DOI: 10.1091/mbc.9.6.1523. View

10.

Ferreira J, Paolella G, Ramos C, Lamond A . Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J Cell Biol. 1998; 139(7):1597-610. PMC: 2132633. DOI: 10.1083/jcb.139.7.1597. View

11.

Cmarko D, Verschure P, Martin T, Dahmus M, Krause S, Fu X . Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol Biol Cell. 1999; 10(1):211-23. PMC: 25164. DOI: 10.1091/mbc.10.1.211. View

12.

Wansink D, Manders E, van der Kraan I, Aten J, VAN Driel R, de Jong L . RNA polymerase II transcription is concentrated outside replication domains throughout S-phase. J Cell Sci. 1994; 107 ( Pt 6):1449-56. DOI: 10.1242/jcs.107.6.1449. View

13.

Pombo A, Hollinshead M, Cook P . Bridging the resolution gap: Imaging the same transcription factories in cryosections by light and electron microscopy. J Histochem Cytochem. 1999; 47(4):471-80. DOI: 10.1177/002215549904700405. View

14.

Besse S, Diaz J, Kindbeiter K, Vigneron M, WARREN S, Kedinger C . Identification of transcription factories in nuclei of HeLa cells transiently expressing the Us11 gene of herpes simplex virus type 1. Gene Expr. 1997; 6(5):315-32. PMC: 6148282. View

15.

Wansink D, 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; 122(2):283-93. PMC: 2119648. DOI: 10.1083/jcb.122.2.283. View

16.

Iborra F, Cook P . The size of sites containing SR proteins in human nuclei. Problems associated with characterizing small structures by immunogold labeling. J Histochem Cytochem. 1998; 46(9):985-92. DOI: 10.1177/002215549804600901. View

17.

Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum L, Phair R . A kinetic framework for a mammalian RNA polymerase in vivo. Science. 2002; 298(5598):1623-6. DOI: 10.1126/science.1076164. View

18.

Misteli T . Protein dynamics: implications for nuclear architecture and gene expression. Science. 2001; 291(5505):843-7. DOI: 10.1126/science.291.5505.843. View

19.

Dahmus M . Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J Biol Chem. 1996; 271(32):19009-12. DOI: 10.1074/jbc.271.32.19009. View

20.

Iborra F, Pombo A, McManus J, Jackson D, Cook P . The topology of transcription by immobilized polymerases. Exp Cell Res. 1996; 229(2):167-73. DOI: 10.1006/excr.1996.0355. View