It has also been shown that the genes which are in a state of transcription are often susceptible to the enzyme DNAase suggesting that the nucleosome organization is atleast temporarily displaced from the region of transcription, presumably due to occupation of transcription sites by RNA polymerase. However, the histone octamer immediately recaptures its position as soon as the transcription is over. The susceptibility of chromatin to DNAase is attributed to lose binding of some nonhistone proteins like HMG14
(HMG = high-mobility group), because, once these proteins are released, the chromatin does not exhibit susceptibility. It has also been shown that some hypersensitive sites (digested with very low concentration of DNAase) are found upstream to the initiation site for transcription. The sites are free of nucleosomes and can be 100-200 bp long.
Another observation with respect to active genes is the linkage of a protein ubiquitin
(ubiquitous presence from bacteria to mammals) to H2A in the form of UH2A in 10-30% nucleosomes. Usually only one of the two H2A molecules of a nucleosome is ubiquitinated. There is a tendency for UH2A to be concentrated in the nucleosomes of the transcribed sequences. There are also evidences of modifications in the DNA due to methylation in inactive genes. Similarly, histone proteins also undergo modifications like acetylation and deacetylation of some histones (H3 and H4) and phosphorylation and dephosphorylation of other histones (H1).
During 1992-93, more information about the role of nucleosome structure in transcription has become available. In Xenopus,
it was shown that placement of a nucleosome (histone octamer) on the 5S gene blocks binding of the transcription factor TFIIIA (consult Expression of Gene : Protein Synthesis 2. Transcription in Prokaryotes and Eukaryotes
for transcription factors). It was also shown that the amino terminal regions of histone molecules are either cleaved off or get heavily acetylated, which allows free access of TFIIIA to nucleosomal DNA. It is believed that either the acetylation releases the amino terminal tails from DNA, thus making it accessible or it induces a conformational change in the nucleosome, which promotes TFIIIA binding.
In view of the above, exact mechanism involving nucleosome changes during activation of genes can not be proposed and only some speculation can be made. More information on this subject will be available in future.