A fundamental question in biology is how a concert of gene expression is orchestrated in a highly packed environment as in eukaryotic nuclei. Gene expression is a continuous process carried out by highly specialized machineries responsible for chromatin remodeling, transcription, RNA processing, RNA export and translation in the cytoplasm (Misteli, 2001; Orphanides and Reinberg, 2002). The process of transcription itself takes place in the nucleus that is a complex organelle both in organization and in function.
Contemporary studies support the concept that the three dimensional organization of the nucleus has a high impact on the functional diversity of the cells (Misteli, 2005), i.e. each gene locus might be characterized by specific nuclear environments. Organization of chromatin in the nucleus is non-random as chromosomes tend to occupy specific regions inside nuclei relative to the nuclear periphery and relative to each other (Parada and Misteli, 2002). The presence of morphologically higher order chromatin domains like euchromatin (loosely packed) and heterochromatin (tightly packed) divides the genome into transcriptionally active and inactive territories, respectively. This view proved to be oversimplistic since a genome wide study by Bickmore and colleagues on the relationship chromatin structureÆ gene activity found instead a correlation gene-rich region: open chromatin structure, gene-poor region: condensed domain, regardless of the activity status of the gene (Gilbert et al., 2004). Chromosomes exist in the nucleus in the form of chromosome territories (Cremer and Cremer, 2001; Parada and Misteli, 2002). The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing.
Chromosome territories are structures permeated by nucleoplasmic channels of various sizes that create large surface areas accessible for regulatory factors to sequences buried within the chromosome territories (Cremer and Cremer, 2001). Various membrane-less nuclear compartments like the nucleolus and distinct nuclear bodies separate functional domains for highly specialized processes like rRNA biogenesis processing, assembly of ribosomal subunits, pre-mRNA splicing, snRNP biogenesis and assembly etc (Fig.1). The cartoon in Fig. 1 represents a static view of the nucleus. Contrary, these domains have been
shown in a series of in vivo experiments to be dynamic structures and, in addition, rapid protein exchange occurs between many of the domains and the nucleoplasm (Misteli, 2001). But there is still a big step from the dynamic nucleus to a multicellular organism with spatial and temporal organization. This implies accomplishment of a complex genetic program initiated at a single cell level (the fertilized egg or zygote) and finalized in multicellular environment in the embryo and adult.
Figure 1 The cell nucleus: organization of the nucleus into specialized domains. The nuclear content is delimited by the nuclear envelope with the nuclear pores serving as transit material between the nucleus and the cytoplasm. The peripheral nuclear lamina regulates the nuclear envelope structure and anchors the interphase chromatin at the nuclear periphery; heterochromatin (inactive chromatin) is associated with the nuclear lamina; PcG bodies, containing polycomb group proteins, are involved in silencing; pre-mRNA splicing factors are localized in nuclear speckles as well as diffusely distributed throughout the nucleoplasm. Transcription sites are observed throughout the nucleoplasm but they have also been shown to be concentrated in one to three compartments termed OPT (Oct1/PTF/transcription) domains; snRNP biogenesis takes place in 1-10 Cajal bodies whereas their Gemini (Gems) might be responsible for snRNP assembly and maturation; Cleavage bodies might be involved in the cleavage and
perinucleolar compartment and the SAM68 nuclear body might play a role in RNA metabolism. PML bodies have been suggested to play a role in aspects of transcriptional regulation and appear to be targets of viral infection (adapted from Spector DL, 2001)
Differential gene expression is the platform that allows formation of cellular diversity necessary for generating multicellular organisms and the physiological relevant substrate in this case is the chromatin (Felsenfeld and Groudine, 2003). The chromatin is a DNA-histone protein complex made up of repeating organizational units called nucleosomes. In a nucleosome a 146 bp double stranded DNA wraps around a central core of eight histone protein molecules (an octamer made of histones H2A, H2B, H3 and H4).
Histone H1 binds to the linker DNA (between two nucleosomes) and fastens the DNA to the nucleosome core. Until recently, our understanding of genetic diseases has been very much related to alteration of the DNA sequence.
In the last decades, chemical modifications of the DNA (methylation) and of histones (methylation, acetylation, phosophorylation, ubiquitination etc.) have been a subject of major interest due to their implication in fundamental cellular and developmental processes (i.e. transcription activation of repression, differentiation, etc.) and found to play a role in many human diseases (Feinberg et al., 2002).
Since epigenetic alterations in human tumours have been discovered in 1983 (Feinberg and Vogelstein, 1983), hundreds of labs have examined their role both in activation of tumour promoter genes as well as silencing of tumour suppressor genes. The combinatorial nature of histone modifications is hypothesized to define a "histone code"
that considerably extends the information potential of the genetic code, giving rise to epigenetic information. Moreover, most core histones consist of several nonallelic variants that can mark specific loci and could play an important role in establishment and maintenance of epigenetic memory. Unravelling the “histone code” is therefore necessary and very challenging since epigenetic mechanisms lie at the very heart of our understanding of stem cell therapy, animal cloning, complex traits and aging.
Model organisms have provided key insights into cellular processes that have been recognized in higher eukaryotes such as humans. I used Drosophila melanogaster as a model organism since it is a well known developmental model system, is easy to handle, the life cycle is short, is subject to easy genetic manipulation, the genome is sequenced and there is an enormous collection of mutants that enable complex experimentation in a living organism.
As a result, most of what we know about the molecular basis of animal development has come from studies of model systems such as Drosophila.