Imaging Transcription in Living Cells

Overview

Journal Annu Rev Biophys

Publisher Annual Reviews

Specialty Biophysics

Date 2009 May 7

PMID 19416065

Citations 63

Authors

Xavier Darzacq

Jie Yao

Daniel R Larson

Sebastien Z Causse

Lana Bosanac

Valeria de Turris

Vera M Ruda

Timothee Lionnet

Daniel Zenklusen

Benjamin Guglielmi

Robert Tjian

Robert H Singer

Affiliations

Soon will be listed here.

Abstract

The advent of new technologies for the imaging of living cells has made it possible to determine the properties of transcription, the kinetics of polymerase movement, the association of transcription factors, and the progression of the polymerase on the gene. We report here the current state of the field and the progress necessary to achieve a more complete understanding of the various steps in transcription. Our Consortium is dedicated to developing and implementing the technology to further this understanding.

Citing Articles

Optogenetic dissection of transcriptional repression in a multicellular organism.

Zhao J, Lammers N, Alamos S, Kim Y, Martini G, Garcia H Nat Commun. 2024; 15(1):9263.

PMID: 39461978 PMC: 11513125. DOI: 10.1038/s41467-024-53539-0.

Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility.

Saxton M, Morisaki T, Krapf D, Kimura H, Stasevich T Sci Adv. 2023; 9(40):eadh4819.

PMID: 37792937 PMC: 10550241. DOI: 10.1126/sciadv.adh4819.

How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription.

Hoboth P, Sebesta O, Hozak P Int J Mol Sci. 2021; 22(13).

PMID: 34206594 PMC: 8269275. DOI: 10.3390/ijms22136694.

Uncoupling of nucleo-cytoplasmic RNA export and localization during stress.

Hochberg-Laufer H, Schwed-Gross A, Neugebauer K, Shav-Tal Y Nucleic Acids Res. 2019; 47(9):4778-4797.

PMID: 30864659 PMC: 6511838. DOI: 10.1093/nar/gkz168.

Quantifying Single mRNA Translation Kinetics in Living Cells.

Morisaki T, Stasevich T Cold Spring Harb Perspect Biol. 2018; 10(11).

PMID: 30385605 PMC: 6211384. DOI: 10.1101/cshperspect.a032078.

References

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

Muller W, Walker D, Hager G, McNally J . Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter. J Cell Biol. 2001; 154(1):33-48. PMC: 2196867. DOI: 10.1083/jcb.200011069. View

Chuang C, Carpenter A, Fuchsova B, Johnson T, de Lanerolle P, Belmont A . Long-range directional movement of an interphase chromosome site. Curr Biol. 2006; 16(8):825-31. DOI: 10.1016/j.cub.2006.03.059. View

Perissi V, Rosenfeld M . Controlling nuclear receptors: the circular logic of cofactor cycles. Nat Rev Mol Cell Biol. 2005; 6(7):542-54. DOI: 10.1038/nrm1680. View

Eskiw C, Rapp A, Carter D, Cook P . RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci. 2008; 121(Pt 12):1999-2007. DOI: 10.1242/jcs.027250. View

Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy S, Phair R . In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol. 2007; 14(9):796-806. PMC: 4942130. DOI: 10.1038/nsmb1280. View

Sugaya K, Vigneron M, Cook P . Mammalian cell lines expressing functional RNA polymerase II tagged with the green fluorescent protein. J Cell Sci. 2000; 113 ( Pt 15):2679-83. DOI: 10.1242/jcs.113.15.2679. View

Pombo A, Jackson D, Hollinshead M, Wang Z, Roeder R, Cook P . Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 1999; 18(8):2241-53. PMC: 1171307. DOI: 10.1093/emboj/18.8.2241. View

Metivier R, Reid G, Gannon F . Transcription in four dimensions: nuclear receptor-directed initiation of gene expression. EMBO Rep. 2006; 7(2):161-7. PMC: 1369254. DOI: 10.1038/sj.embor.7400626. View

10.

Shav-Tal Y, Darzacq X, Shenoy S, Fusco D, Janicki S, Spector D . Dynamics of single mRNPs in nuclei of living cells. Science. 2004; 304(5678):1797-800. PMC: 4765737. DOI: 10.1126/science.1099754. View

11.

Kino T, Liou S, Charmandari E, Chrousos G . Glucocorticoid receptor mutants demonstrate increased motility inside the nucleus of living cells: time of fluorescence recovery after photobleaching (FRAP) is an integrated measure of receptor function. Mol Med. 2005; 10(7-12):80-8. PMC: 1431369. DOI: 10.2119/2005-00026.Kino. View

12.

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

13.

Zipfel W, Williams R, Webb W . Nonlinear magic: multiphoton microscopy in the biosciences. Nat Biotechnol. 2003; 21(11):1369-77. DOI: 10.1038/nbt899. View

14.

Phair R, Misteli T . High mobility of proteins in the mammalian cell nucleus. Nature. 2000; 404(6778):604-9. DOI: 10.1038/35007077. View

15.

Karpova T, Chen T, Sprague B, McNally J . Dynamic interactions of a transcription factor with DNA are accelerated by a chromatin remodeller. EMBO Rep. 2004; 5(11):1064-70. PMC: 1299176. DOI: 10.1038/sj.embor.7400281. View

16.

Meijsing S, Elbi C, Luecke H, Hager G, Yamamoto K . The ligand binding domain controls glucocorticoid receptor dynamics independent of ligand release. Mol Cell Biol. 2007; 27(7):2442-51. PMC: 1899895. DOI: 10.1128/MCB.01570-06. View

17.

Sprague B, Pego R, Stavreva D, McNally J . Analysis of binding reactions by fluorescence recovery after photobleaching. Biophys J. 2004; 86(6):3473-95. PMC: 1304253. DOI: 10.1529/biophysj.103.026765. View

18.

Carter D, Eskiw C, Cook P . Transcription factories. Biochem Soc Trans. 2008; 36(Pt 4):585-9. DOI: 10.1042/BST0360585. View

19.

Bres V, Yoh S, Jones K . The multi-tasking P-TEFb complex. Curr Opin Cell Biol. 2008; 20(3):334-40. PMC: 2628440. DOI: 10.1016/j.ceb.2008.04.008. View

20.

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