Space exploration by the promoter of a long human gene during one transcription cycle

Nucleic Acids Res. 2013 Feb 1;41(4):2216-27. doi: 10.1093/nar/gks1441. Epub 2013 Jan 8.

Abstract

An RNA polymerase has been thought to transcribe by seeking out a promoter, initiating and then tracking down the template. We add tumor necrosis factor α to primary human cells, switch on transcription of a 221-kb gene and monitor promoter position during the ensuing transcription cycle (using RNA fluorescence in situ hybridization coupled to super-resolution localization, chromosome conformation capture and Monte Carlo simulations). Results are consistent with a polymerase immobilized in a 'factory' capturing a promoter and reeling in the template, as the transcript and promoter are extruded. Initially, the extruded promoter is tethered close to the factory and so likely to re-initiate; later, the tether becomes long enough to allow re-initiation in another factory. We suggest close tethering underlies enhancer function and transcriptional 'bursting'.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cells, Cultured
  • DNA-Directed RNA Polymerases / metabolism*
  • Human Umbilical Vein Endothelial Cells / metabolism
  • Humans
  • In Situ Hybridization, Fluorescence
  • Models, Genetic
  • Monte Carlo Method
  • Promoter Regions, Genetic*
  • RNA / analysis
  • Repressor Proteins / biosynthesis
  • Repressor Proteins / genetics
  • Templates, Genetic
  • Transcription, Genetic*

Substances

  • Repressor Proteins
  • SAMD4A protein, human
  • RNA
  • DNA-Directed RNA Polymerases