PhD Defense Aafke van den Berg: 'The interplay between polymerase organization and nucleosome occupancy on genes'



12:30 hrs


Aula, TU Delft


The transfer of information from DNA to other molecules is central to every living system. During transcription the enzyme 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. RNAP competes for space with many proteins such as other RNAPs and histones, which are essential for the protection of DNA. During transcription histones form roadblocks to RNAP and RNAP evicts histones. We use theoretical modeling to show that these interactions lead to the formation of RNAP pelotons along the DNA.  Interestingly, this process is comparable to peloton formation in a completely different system: cycling races. Cyclists (RNAPs) form pelotons to reduce the air resistance (the histones).  Further, we show that histones can be replaced by other proteins after being evicted by RNAP.  The theoretical predictions in this thesis shed new light on many experimental observations and we expect to see peloton formation in many different systems where motors interact with dynamic roadblocks.