Phasing and modification of nucleosomes in active genes

Content
Organization of Genetic Material 1.  Packaging of DNA as Nucleosomes in Eukaryotes
Techniques leading to nucleosome discovery
Subunit of chromatin - the nucleosome
Spatial arrangement of histones
Relation between different nucleosomes
Solenoid model
Loops, domains and scaffolds in chromatin
Chromatin replication and nucleosome assembly
Phasing and modification of nucleosomes in active genes
Phasing and Modification of Nucleosomes in Active Genes
Active and inactive chromatin have been compared with respect to nucleosome organization. It is shown that nucleosome in the form of repeats are present in both cases, but in active form, the chromatin contains nonhistones in addition to histones. These non-histones may modify the structure of nucleosomes to a more opened out form, so that they become increasingly sensitive to nucleases.

Some specificity in the distribution of DNA sequences on the nucleosomes and a lack of their random distribution is called nucleosome phasing. Recent evidence suggested that nucleosomes are really phased along the length of DNA and that through their position on DNA, regulatory proteins may expose or protect certain DNA sequences. The spacing of nucleosomes is not random in statistical sense, but is rather regular and non-random. It has also been shown that spacing of nucleosomes may vary in different tissues, suggesting that the locations of nucleosomes are not constant but may vary. In the chromosomes of SV40, a DNA segment of 400 base pairs encompassing the replication region and promoters is naked, completely devoid of nucleosomes, showing phasing of nucleosomes. In several other genes at 5' end, naked regions of DNA have been described, suggesting that active genes may have to uncoil and lose their nucleosome structure temporarily, thus providing a mechanism for regulation of gene activity.

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 and HMG17 (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.