Research

How does the packaging required to fit the 16MB Candida genome within this cell help to control gene expression?

To view references click here.

Order in living systems is both obvious and elusive [2]. The degree to which we recognise order depends upon the techniques that we use to test our hypotheses. Nowhere is this truer than our understanding of the nucleus. Long regarded as a bag of randomly intermingled chromosomes, the nucleus in fact contains numerous non-membrane bound sub-compartments that are essential for the coordination of the information encoded by the genome.

Cytological studies have demonstrated that the apparent sub-compartmentalisation of the nucleus plays a role in coordinating the first step of gene expression, the production of mRNA. These studies have identified distinct focal points within the nucleus where RNA is actively produced by RNA polymerases [8-11]. These focal points, called transcription factories, are apparently associated with multiple genes [8, 9, 11, 12]. These studies have led to the proposal of 3-dimensional models for the regulation of gene expression in which similarly regulated genes loop out of repressive chromatin zones (chromosome territories) to enable the formation of transcription factories (Figure 1; [3-7]).

3-dimensional models of gene regulation require that the cis- and trans-regulatory sequences of one or multiple genes are in close spatial proximity. Such models begin to explain the non-random arrangement of genes within eukaryotic chromosomes [2, 4, 16, 18, 19, 22, 23] and positional effects on transcription [24]. Furthermore, the looping of transcriptional units, and the transcription of groups of genes within a factory [25], would minimise fluctuations in the concentrations of regulatory factors and hence transcriptional noise [26].

It has been postulated that transcription factory formation within a group of genes, on one chromosome, is more likely than between genes on different chromosomes (Figure 1 [12]). This is supported by observations of the clustering of similarly expressed, functionally related genes within chromosomes [13]. The inter-species conservation of such groupings indicates that they are under evolutionary pressure to be maintained[4, 14, 15], although not necessarily on a particular chromosome [13, 16, 17]. Hence the question: do physical constraints on transcription factory and gene loop formation explain the maintenance of functionally related gene groupings?

The movement of gene loops into specific nuclear domains would enable the formation of factories and the transcription of tissue specific genes at one or several places within the nucleus. This type of coordination may play a major role in development, explaining the apparent lack of linear clustering of tissue specific genes [18], despite evidence for pathway specific clustering [19]. Experimental observations [12, 20] indicate that inter-chromosomal interactions may occur, possibly explaining trans-sensing or transvection [21]. However, it is still unclear whether there are designated areas within sub-nuclear domains for the control of specific gene families [5, 6, 12].

Gene looping acts to increase and stabilise the accessibility of regulatory sequences to diffusing transcription factors [7], therefore loop formation or movement must be coordinated if it is to have a significant role in gene regulation. Current results indicate that chromatin movement is dependent on the cell cycle [27, 28] and can be either an active [27, 28] or passive process [29, 30], which is not due to the act of transcription itself [12, 31-33]. Despite this we know that the proximity of different chromosomal (e.g. centromere [28, 29]) or nuclear (e.g. nucleolus [30]) structures limit the movement of chromosomal regions. Hence, we are left with the following questions: 1) how is the formation of the transcription factories and associated gene loops regulated? 2) Are these conformations dependent on chromatin or DNA features or the transcription machinery, but not transcription itself?

Simply, life is more than DNA. DNA cannot act as a blue-print for life in the absence of other factors. Coordinated changes to gene expression are central to cellular metabolism, development and disease. However, we will never truly understand gene expression or how that expression alters with the 4th dimension (time), until we understand the 3-dimensional interactions that occur around, within and between genes. Therefore, we are currently testing the hypothesis that the spatial positioning of genes within the nucleus coordinates the reading of information within a genome. In part, this includes identifying and understanding the mechanisms by which 3-dimensional interactions occur around, within and between genes. We believe that this will increase our understanding of gene expression, enabling us to begin to comprehend the mechanisms that coordinate this process over time. As such, it will have a significant impact on our understanding of the dynamics of biological systems, development and disease.

To view references click here.