Your question reveals a linear cascade of events positioning DNA at the end of this process. This model is not valid. Find conditions where the DNA is in the cytoplasm and then ask how transcription occurs. Ectopic expression of a piece of DNA– how is it transcribed? And why you are so interested to Histones?

We can detect histones even in the cytoplasm or even extracellular. Why histones is a barrier for you? Cell is a dynamic structure.

Transcription is a multistep process that starts with the assembly of the pre-initiation complex, the recruitment of the Pol II Holoenzyme, the initiation of transcription, the transition to elongation (up to now everything happens at the promoter), elongation and termination of transcription. Very early it has been found that pre-initiation complex formation (especially TFIID) requires the absence of nucleosomes at the promoter, while elongation can take place in the presence of nucleosomes. (see e.g. Workman, J. L., & Roeder, R. G. (1987). Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell, 51(4), 613–622.)

Dear Ho-Ryun, What you descibed is nice but this is not the answer to the question and I am sure that this model applies only in the text books and in ppts. Too much energy too much time and no one coordination in response to signal. It is a good model for publications but if you want to explain how coordinated transcription occurs when you add 1µM of Dex and/or 1µ.M of Dex+TPA in naive cels or in memory cells then your linear assembly that you descibed  seems to me a very complicate process. In addition, what happens when transcription occurs in M-phase? Lets say that a viral DNA  decides to be transcribed in M ?  and what happens if the piece of DNA decides to get transcribed in the cytoplasm?  Regards, Vasilis

@Vassilis- viral DNA is not controlled by histones, and is not relevant to this question. The vast majority of transcription is inhibited in M phase. Histone reorganization IS complex, and may not follow a linear path, but it nonetheless regulates transcription, and must be displaced to permit transcription.

Dear Daniel, I do not agree with your statement. Integration of viral DNA  to chromosomes implies that viral DNA is part of the genome of the cell and follows the rules.  For DNA viruses, silent long term adenovirus infection should impose adeno-DNA organization in nucleosomes like structures. But viral DNA is transcribed and this happens in the nucleus, in the cytoplasm, in M-phase or why not extracellular. I agree that in M phase transcription is in principle off, but the exceptions help us to understand the rules. So, I do not agree that displacement of histones is essential to permit transcription.

In transcription we have to distinguish, the-activated memorized cells (cells that receive the same signal routinely), naïve cells that receive a NEW signal, housekeeping genes that undergo slow basic transcription and signal activated cells that need to be COORDINATED. The classical image with the recruitment of the Pol II Holoenzyme, the initiation of transcription, the transition to elongation (up to now everything happens at the promoter), elongation and termination of transcription, this is TO MY OPINION an OLD OLD story. It may happen but does not mean that this is the way the signal is coordinated to promote transcription.

DNA processing, Transcription and Translation are and should be coordinated under signal activation in eukaryotic cells and this implies that nothing happens on the basis of the linear histone-nucleosome displacement in order to liberate the “VIRGIN” promoter so to activate transcription. ALL PIECES of DNA have a memory and the cell has a memory. THE topological properties of these MOLECULES are critical in the coordination of the signal and this is why if you have a cell culture and you add a ligand (i.e. Dex) only a subset of these cells respond and if you keep these cells for few passages no one is going to respond and, thus, the majority of related papers could be artifacts.

PS.  If you are in London and your friend is in Paris then the coordination, activation of transcription, in London and in Paris, can be done if the decision occurs in London?, in Paris? or in the USA? And this transcription cannot be done if Moscow or Berlin do not agree and this has nothing to do with the positioning of the nucleosome in London and Paris promoters but only with the related “memory” of the implicated partners and the Signal. Regards, Vassilis

I think the point is that chromatin architecture is dynamic. Histones and TFs are in competition, and rapid exchange. The memory phenomenon is what drives the entire field of epigenetic regulation of gene expression. Yes, history of expression matters, and this is encoded by histone modifications, nucleosomal occupancy, and in some cases DNA methylation. That doesn't mean that the essential model that nucleosomes inhibit RNAPII recruitment and elongation is wrong. It is a false dichotomy, in most cases, to argue that a promoter is fully nucleosomal, or fully open. Transcription is happening at burst that reflect transient sampling of different epigenetic states, in concert with recruitment of histone remodelers and competition between histone and TFs for DNA binding.

@Daniel, That statement looks to me much better even though chromatin is only part of the cell story. TFs and other macromolecular complexes as also nucleosomes etc are transient "transporters" of cell - DNA and signal memories that function in coordination with the Proteaome-Ub / systems to control transcription, DNA processing and translation upon Signal activation. This system needs to be coordinated. Who is doing the coordination is another question.

Epigenetic potential is nothing else than the memory of a short or long event (depends on the origin/potential of the signal) that once happened. This epigenetic history should be TRANSMITTED from cell to cell. To switch off the cell memory we need to activate Stem cell activation(s) and this is not an easy going event. Histones displacement is a barrier, as it is the nuclear membrane - a system of control but that does not mean that signals cannot bypass the barriers. This suggests that cell boundaries are not delimited by cell membranes. Regards, Vassilis

Dear All,

Thanks a lot for this healthy debate. But, to my poor understanding, there is no clear answer yet. The situation seems even more complicated now. My question was very simple. DNA is generally woven around histones. When RNA Polemerase II reaches the promotor region, is it necessary for the promotor to be histone free? what is the situation inside the transcription bubble? and what about the rest of the DNA for that particular gene?

If the answer to histone removal is yes, what impact would histone modifications have on transcription?

To my understanding nucleosome-remodelling complexes must remove the histones from promoter region to facilitate binding of RNA Pol II, but what Ho-Ryun Chung mentioned is a little confusing. RNA Pol II would require a single stranded DNA in its active site for transcription, I was just wondering how could transcription proceed (i.e., elongation) if the DNA is still bound to histones??

Yes, elongating RNAPII can displace histones. Subsequently, these histones can rapidly reassemble after the transcription bubble has passed. There is not a pre-requisite for histones to be cleared from the gene body in order for transcription to proceed.

Recruitment of RNAPII to enhancers or promoters is mediated by transcription factors, and these factor bind in a mutually exclusive way with histones. So for the initiation of transcription, histone modifications and displacement are likely far more important than for elongation.

Dear Daniel, thanks a lot. That was a very clear answer indeed. One more thing, what is basically affected/influenced by histone modification??? is it the primary transcription factors? or nucleosome remodeling complexes? as histone modification might influence transcription of a gene. In addition, where does this modification take place, only in the promoter region or can be anywhere in the entire gene sequence?

Histone modifications are dependent on enzymatic activities that are not intrinsically sequence dependent. Factors such as HATs or HDACs get recruited to DNA by transcription factors. As such it is the sequence specific DNA binding factors that help establish where histone epigenetic marks will occur. However, the process is a bit circular; histone modifications in turn regulate DNA accessibility, and can therefore feedback to regulate TF occupancy.

Cis-acting regulatory DNA elements are not limited to promoters; examples of intronic enhancers are quite common, and histone marks such as H3K9 or H3K27acetylation can therefore be found within gene bodies. Marks such as H3K36 methylation are broadly enriched over actively expressed genes. There is no general answer here; the genomic distribution of histone modifications depends entirely on the specific type of modification in question, as does its proposed function.