Transcription Factories

Overview

Journal Front Genet

Date 2012 Oct 31

PMID 23109938

Citations 57

Authors

Dietmar Rieder

Zlatko Trajanoski

James G McNally

Affiliations

Soon will be listed here.

Abstract

There is considerable evidence that transcription does not occur homogeneously or diffusely throughout the nucleus, but rather at a number of specialized, discrete sites termed transcription factories. The factories are composed of ~4-30 RNA polymerase molecules, and are associated with many other molecules involved in transcriptional activation and mRNA processing. Some data suggest that the polymerase molecules within a factory remain stationary relative to the transcribed DNA, which is thought to be reeled through the factory site. There is also some evidence that transcription factories could help organize chromatin and nuclear structure, contributing to both the formation of chromatin loops and the clustering of active and co-regulated genes.

Citing Articles

Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3.

Ryczek N, Lys A, Wanowska E, Kozlowska-Maslon J, Makalowska I Commun Biol. 2025; 8(1):391.

PMID: 40057624 PMC: 11890862. DOI: 10.1038/s42003-025-07815-4.

Transcription factor condensates, 3D clustering, and gene expression enhancement of the regulon.

Lee J, Simpson L, Li Y, Becker S, Zou F, Zhang X Elife. 2024; 13.

PMID: 39347738 PMC: 11441978. DOI: 10.7554/eLife.96028.

An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution.

An J, Brik Chaouche R, Pereyra-Bistrain L, Zalzale H, Wang Q, Huang Y Proc Natl Acad Sci U S A. 2024; 121(28):e2400737121.

PMID: 38968127 PMC: 11252963. DOI: 10.1073/pnas.2400737121.

Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome.

Pletenev I, Bazarevich M, Zagirova D, Kononkova A, Cherkasov A, Efimova O Nucleic Acids Res. 2024; 52(11):6234-6252.

PMID: 38647066 PMC: 11194087. DOI: 10.1093/nar/gkae271.

An emerging paradigm in epigenetic marking: coordination of transcription and replication.

Fenstermaker T, Petruk S, Mazo A Transcription. 2024; 15(1-2):22-37.

PMID: 38378467 PMC: 11093037. DOI: 10.1080/21541264.2024.2316965.

References

Dundr M . Nuclear bodies: multifunctional companions of the genome. Curr Opin Cell Biol. 2012; 24(3):415-22. PMC: 3372688. DOI: 10.1016/j.ceb.2012.03.010. View

Guthold M, Zhu X, Rivetti C, Yang G, Thomson N, Kasas S . Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. Biophys J. 1999; 77(4):2284-94. PMC: 1300507. DOI: 10.1016/S0006-3495(99)77067-0. View

Taddei A, Schober H, Gasser S . The budding yeast nucleus. Cold Spring Harb Perspect Biol. 2010; 2(8):a000612. PMC: 2908769. DOI: 10.1101/cshperspect.a000612. View

Marshall N, Price D . Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol Cell Biol. 1992; 12(5):2078-90. PMC: 364379. DOI: 10.1128/mcb.12.5.2078-2090.1992. View

Fedorova E, Zink D . Nuclear genome organization: common themes and individual patterns. Curr Opin Genet Dev. 2009; 19(2):166-71. DOI: 10.1016/j.gde.2009.02.003. View

Jackson D, Cook P, Patel S . Attachment of repeated sequences to the nuclear cage. Nucleic Acids Res. 1984; 12(17):6709-26. PMC: 320111. DOI: 10.1093/nar/12.17.6709. View

Cook P . Predicting three-dimensional genome structure from transcriptional activity. Nat Genet. 2002; 32(3):347-52. DOI: 10.1038/ng1102-347. View

Jackson D, McCready S, Cook P . RNA is synthesized at the nuclear cage. Nature. 1981; 292(5823):552-5. DOI: 10.1038/292552a0. View

Schoenfelder S, Sexton T, Chakalova L, Cope N, Horton A, Andrews S . Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet. 2009; 42(1):53-61. PMC: 3237402. DOI: 10.1038/ng.496. View

10.

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

11.

Harada Y, Funatsu T, Murakami K, Nonoyama Y, Ishihama A, Yanagida T . Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys J. 1999; 76(2):709-15. PMC: 1300075. DOI: 10.1016/S0006-3495(99)77237-1. View

12.

Martin S, Pombo A . Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res. 2003; 11(5):461-70. DOI: 10.1023/a:1024926710797. View

13.

Chubb J, Trcek T, Shenoy S, Singer R . Transcriptional pulsing of a developmental gene. Curr Biol. 2006; 16(10):1018-25. PMC: 4764056. DOI: 10.1016/j.cub.2006.03.092. View

14.

Tokunaga M, Imamoto N, Sakata-Sogawa K . Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat Methods. 2008; 5(2):159-61. DOI: 10.1038/nmeth1171. View

15.

Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E . Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006; 38(11):1348-54. DOI: 10.1038/ng1896. View

16.

Saitoh N, Sakamoto C, Hagiwara M, Agredano-Moreno L, Jimenez-Garcia L, Nakao M . The distribution of phosphorylated SR proteins and alternative splicing are regulated by RANBP2. Mol Biol Cell. 2012; 23(6):1115-28. PMC: 3302738. DOI: 10.1091/mbc.E11-09-0783. View

17.

Jackson D, Cook P . Transcription occurs at a nucleoskeleton. EMBO J. 1985; 4(4):919-25. PMC: 554280. DOI: 10.1002/j.1460-2075.1985.tb03719.x. View

18.

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

19.

Papantonis A, Cook P . Fixing the model for transcription: the DNA moves, not the polymerase. Transcription. 2011; 2(1):41-4. PMC: 3023647. DOI: 10.4161/trns.2.1.14275. View

20.

Osborne C, Chakalova L, Mitchell J, Horton A, Wood A, Bolland D . Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol. 2007; 5(8):e192. PMC: 1945077. DOI: 10.1371/journal.pbio.0050192. View