Definition of Chromatin
In eukaryotes, on the contrary of prokaryotes, the DNA is packaged in the form of a nucleoprotein complex called "chromatin", which carries the hereditary message. It is located in a nucleus and is organised in several separate entities, the chromosomes.
The Concept of Heterochromatin
In 1928, based on histological observations, Emil HEITZ defined heterochromatin
(HC) as being the chromosomal segments which appear extremely condensed and
dark in colour in the interphase nucleus. In fact, chromatin consists of a tangle
of fibres, the diameter of which not only vary during the cell cycle, but also
depend on the region of the chromosome observed.
The active euchromatin consists of a fibre with a diameter corresponding
to that of a nucleosome, a double strand DNA segment, wound around homodimers
of the histones H2A, H2B, H3, and H4 . In inactive euchromatin, this fibre can
wind itself into a solenoid thanks to histones H1. It is further organised through
interactions with non-histone proteins (topoisomerase II, scaffold protein 2,
lamins...). As regards the heterochromatin, as defined above, its constituent
fibre is more condensed and often appears to be composed of aggregates. It involves
numerous additional proteins, including the HP1 proteins (Heterochromatin Protein 1).
There are two types of heterochromatin,
and facultative HC, which differ slightly, depending on the DNA
that they contain. The richness in satellite DNA determines the permanent or reversible nature of the heterochromatin, its polymorphism and its staining properties.
Despite the differences described above, constitutive HC and facultative HC have very similar properties
This is in fact what defines heterochromatin, and it is applicable to both constitutive HC and facultative HC. This high condensation renders it strongly chromophilic and inaccessible to DNAse 1 and to other restriction enzymes in general.
The incorporation of various nucleotide analogues shows that the DNA from both constitutive and facultative HC, is late replicating. HC late replication results, on the one hand, from its high degree of condensation, which prevents the replicating machinery from easily accessing the DNA, and, on the other hand, from its location in a peripheral nuclear domain that is poor in active elements.
Histones may undergo post-translational modifications of their N-terminal ends which may affect the genetic activity of the chromatin.
Methylation of the histone H3 lysine 9 (H3-K9) has only very recently been found to be involved in the process of heterochromatinisation of the genome, both in constitutive and facultative HC.
The study of various organisms has shown that constitutive HC has a genuine tendency to aggregate during interphase.
Certain observations have led to the identification of various elements that have an important role in the formation of heterochromatin, be it constitutive or facultative.
Large repetitions of transgenes do not all lead to a transcriptional inactivation of the transgene. The silencing induced by tandem repeats appears to be linked to the presence of prokaryotic DNA sequences, rich in CpG, likely to be methylated. Then the base composition of the tandem repeats could therefore play an important role in the formation of heterochromatin.
We have seen that hypo-acetylation of histones is a characteristic of silent chromatin, whether it is heterochromatin or not. Thus, blocking the de-acetylation of the histones by adding trichostatine A induces hyper-acetylation of the histones, which causes a more open chromatin structure.
Methylation of the histone H3 on lysine 9 is an epigenetic modification that has recently been shown to be involved in the process of heterochromatinisation, not only in constitutive HC but also on the inactive X. The enzyme responsible for this methylation is the histone methyltransferase SUV39H1.
The HP1 proteins do appear to have a particular role in the organisation of heterochromatin. Studies of the variegation by position effect (PEV effect) in Drosophila and studies of transgenes in Drosophila and mouse have allowed a better understanding of the role of these proteins.
HP1 proteins appear to be an essential link in the formation of heterochromatin, and could have the role of chromatin domain organisers. These proteins appear to be able to recognise particular structures that are created by the pairing and/or the association of repeated DNA sequences. In addition, thanks to the chromodomain (CD) and the chromoshadow domain (CSD), they are able to establish secondary interactions with a large number of other proteins.
The precise role of heterochromatin in the human genome long remained a mystery, as its frequent polymorphisms did not appear to have any functional or phenotypic effect.
In most eukaryotes, the centromeres are loaded with a considerable mass of heterochromatin. It has been suggested that centromeric HC is necessary for the cohesion of sister chromatids and that it allows the normal disjunction of mitotic chromosomes.
Gene expression may be controlled at two levels:
Mechanism of inactivation in cis :
Following a chromosomal rearrangement, a euchromatic region may
be juxtaposed with a heterochromatic region. Where the rearrangement removes
certain normal barriers that protect the euchromatin, the heterochromatic
structure is able to propagate in cis to the adjacent euchromatin,
thus inactivating the genes contained therein. This mechanism has been observed in position effect variegation (PEV) in Drosophila and also in the inactivation of certain transgenes in mouse.
Mechanism of inactivation in trans :
During cell differentiation, certain active genes are likely to be transposed
into a heterochromatic nuclear domain, thus causing them to become inactive. Such a mechanism has been proposed as an explanation for the co-localisation in lymphocyte nuclei of the protein IKAROS and the genes of which it controls the expression, with centromeric heterochromatin.
These diseases are generally the result of an alteration in the process of cell differentiation.
In conclusion, although heterochromatin is apparently amorphous and isolated at the periphery of the nucleus, it appears to have an absolutely essential role in the organisation and function of the genome.
Throughout this review we have mainly presented the characteristics linked with heterochromatin, be it constitutive or facultative. We have shown that the properties of constitutive HC are not fundamentally different from those of facultative HC. It therefore seems clear that the mechanisms involved in facultative heterochromatinisation, which are epigenetic mechanisms, are the same mechanisms that intervene in the repression of euchromatin in general.
Mattei MG, Luciani J
Atlas of Genetics and Cytogenetics in Oncology and Haematology 2003-01-01
Heterochromatin, from Chromosome to Protein
Online version: http://atlasgeneticsoncology.org/teaching/30078/heterochromatin-from-chromosome-to-protein