Nucleosome displacement

The structure of the promoter region of some of the genes studied overlaps a nucleosome in such a way that the RNA polymerase II cannot get to its binding site. The interaction between the receptor dimers and the HRE causes the nucleosomes to have their structures altered, either by being displaced or by having their structure come partly undone. This change in the configuration permits the fixation of the RNA polymerase II, with which the transcription can be initiated. 

These results raise the prospect of dynamics of nucleosomes in linker histone-free chromatin, that is, of a thermal fluctuation of nucleosomes between closed negative , open , and closed positive states identified in the minicircle system. If this equilibrium exists, an extra supercoiling constraint applied to the fiber should displace it in one direction or the other depending on the sign of that constraint, and this displacement should be reversible upon its removal. 

O Donohue, M.F., Duband-Goulet, I., Hamiche, A., and Prunell, A. (1994) Octamer displacement and redistribution in transcription of single nucleosomes. Nucleic Acids Res. 22, 937-945. Studitsky, V.M., Clark, D.J., and Felsenfeld, G. (1994) A histone octamer can step around a transcribing polymerase without leaving the template. Cell 76, 371-382. 

The process of nucleosome remodeling, with the exception of that mediated by RNA polymerase II [111], often leads to the displacement of the histone octamer from one segment of the DNA to another. For the ISWI and dMi-2 containing complexes transfer only in cis, but not in trans has been observed [48]. 

Fig. 5. Proposed mechanism of passive cis-displacement of a histone octamer by a transcribing SP6 RNA polymerase or RNA polymerase III. (Adapted with permission from Ref. [109].) A. The transcribing polymerase III approaches a nucleosome. B. The nucleosomal DNA is partially unwrapped, a loop containing the polymerase is formed, and the DNA behind the polymerase binds to the vacated histones. C. The octamer is reformed in a new position behind the polymerase.

Langst, G., Bonte, E.J., Corona, D.F., and Becker, P.B. (1999) Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97, 843-852. 

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.

DNA, since proximity eflfects demand that the DNA or nascent RNA closest to the histones at the point of disruption will be the polyanion for which those histones will preferentially reassociate. Ten Heggeler-Bordier et al. [95] have verified these observations. They used immuno-electron microscopy to determine what happens to histones after transcription with T7 RNA polymerase of a multi-nucleosomal template and also observed transfer to the nascent RNA. In contrast, Kirov et al. [96] have reported that no histones displace during transcription with this polymerase. However, as described above, transcriptional efficiency and ultimately histone displacement is not efficient in very low ionic strength conditions. 

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... 

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