The interplay between polymerase organization and nucleosome occupancy along DNA: How dynamic roadblocks on the DNA induce the formation of RNA polymerase pelotons

Aafke van den Berg

Research output: ThesisDissertation (TU Delft)

36 Downloads (Pure)

Abstract

During transcription RNA polymerase (RNAP) moves along a DNA molecule to copy the information on the DNA to an RNA molecule. Many textbook pictures show an RNAP sliding along empty DNA, but in reality it is crowded on the DNA and RNAP competes for space with many proteins such as other RNAP’s and histones. Coverage of DNA by histones is essential for DNA protection and signaling. However, during transcription RNAP evicts histones, which then rebind quickly or are replaced by other proteins. How does crowding of RNAP and histones on the DNA affects transcription dynamics on the one hand, and how does transcription activity change the density and exchange of histones along the DNA on the other hand? Those are the central questions of this thesis.
Original languageEnglish
Awarding Institution
  • Delft University of Technology
Supervisors/Advisors
  • Dekker, N.H., Supervisor
  • Depken, S.M., Advisor
Thesis sponsors
Award date29 Sep 2017
Print ISBNs978-90-8593-308-3
DOIs
Publication statusPublished - 2017

Keywords

  • Transcription
  • transcriptional bursts
  • TASEP
  • Crowding
  • Nucleosomes
  • Bus route model

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