Transcription models disruptive

Fig. 1. Two models to describe the process of transcription through nucleosomes. The spooling model is taken from Studitsky et al. [89]. The RP (RNA polymerase) is shown to cause octamer displacement from the DNA that is being transcribed. The octamer is transferred to the DNA that was previously transcribed which occurs in a series of eight steps. The disruptive model is taken from van Holde et al. [3]. The octamer is shown to be disrupted in a series of steps (A-E) in which the two H2A, H2B dimers are displaced by the RNA polymerase and subsequently shown to reassociate after the polymerase has passed.

The model of Fig. IB is taken from a review by van Holde et al. [3] which I refer to as the disruptive model. In this model the polymerase causes conditions (step A) which promote not only the displacement of the entry site H2A, H2B dimer from DNA, but also from the H3, H4 tetramer (step B). As a result of this disruption, the polymerase is free to transcribe through the tetramer alone without a general displacement from its associated DNA (step C). The H2A, H2B dimer is now free to reassociate to the vacated entry site (step D) to re-establish contacts with both the DNA and the H3, H4 tetramer. As transcription proceeds into the exit site H2A, H2B dimer, these proteins are now displaced from both the DNA and the H3, H4 tetramer in a similar manner as the entry site H2A, H2B dimer (step E). A positive feature with regard to this model is that by displacement of H2A, H2B, the polymerase is able to transcribe the DNA with half the histones displaced prior to transcription. Therefore both models, spooling and disruptive , describe mechanisms which would favorably enhance the process of transcription. Support for the disruptive model comes from the substantial in vivo information which suggests that nucleosomes undergo substantial disruption during transcription, as was described in the previous section. Of particular note are those observations which indicate that a discrete population of H2A, H2B... 

FIGURE 26-7 Model for p-independent termination of transcription in f. coli. RNA polymerase pauses at a variety of DNA sequences, some of which are terminators. One of two outcomes is then possible the polymerase bypasses the site and continues on its way, or the complex undergoes a conformational change (isomerization). In the latter case, intramolecular pairing of complementary sequences in the newly formed RNA transcript may form a hairpin that disrupts the RNA-DNA hybrid and/or the interactions between the RNA and the polymerase, resulting in isomerization. An A=U hybrid region at the 3 end of the new transcript is relatively unstable, and the RNA dissociates completely, leading to termination and dissociation of the RNA molecule. This is the usual outcome at terminators. At other pause sites, the complex may escape after the isomerization step to continue RNA synthesis. 

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