In genetics, transcription factories describe the discrete sites where transcription occurs in the nucleus. They were first discovered in 1993 and have been found to have structures analogous to replication factories, sites where replication also occurs in discrete sites. The factories contain an RNA polymerase (active or inactive) and the necessary transcription factors (activators and repressors) for transcription. Transcription factories containing RNA polymerase II are the most studied but factories can exist for RNA polymerase I and III; the nucleolus being seen as the prototype for transcription factories. It is possible to view them under both light and electron microscropy. The discovery of transcription factories has challenged the original view of how RNA polymerase interacts with the DNA polymer and it is thought that the presence of factories has important effects on gene regulation and nuclear structure.
The first use of the term ‘transcription factory’ was used in 1993 by Jackson and his colleagues who noticed that transcription occurred at discrete sites in the nucleus. This contradicted the original view that transcription occurred at an even distribution throughout the nucleus.
The structure of a transcription factory appears to be determined by cell type, transcriptional activity of the cell and also the method of technique used to visualise the structure. The generalised view of a transcription factory would feature between 4 – 30 RNA polymerase molecules and it is thought that the more transcriptionally active a cell is, the more polymerases that will be present in a factory in order to meet the demands of transcription. The core of the factory is porous and protein rich, with the hyperphosphorylated, elongating form polymerases on the perimeter. The type of proteins present include: ribonucleoproteins, co-activators, transcription factors, RNA helicase and splicing and processing enzymes. A factory only contains one type of RNA polymerase and the diameter of the factory varies depending on the RNA polymerase featured; RNA polymerase I factories are roughly 500 nm in width whereas RNA polymerase II and III factories a magnitude smaller at 50 nm. It has been experimentally shown that the transcription factory is immobilised to a structure and it is postulated that this immobilisation is because of a tethering to the nuclear matrix; this is because it has been shown it is tied to a structure that is unaffected by restriction enzymes. Proteins that have been thought to be involved in the tethering includes spectrin, actin and lamins.
The structure of a transcriptional factory directly relates to its function. Transcription is made more efficient because of the clustered nature of the transcription factory. All the necessary proteins: RNA polymerase, transcription factors and other co-regulators are present in the transcription factory that allows for faster RNA polymerisation when the DNA template reaches the factory, it also allows for a number of genes to be transcribed at the same time.
The amount of transcription factories found per nucleus appears to be determined by cell type, species and the type of measurement. Cultured mouse embryonic fibroblasts have been found to have roughly 1500 factories through immunofluorescence detection of RNAP II however cells taken from different tissues of the same mouse group had between 100 and 300 factories. Measurements of the number of transcription factories in HeLa cells give a varied result. For example, using the traditional fluorescence microscopy approach 300 – 500 factories were found but using both confocal and electron microscopy roughly 2100 were detected.
In addition to the specialisation factories have for the type of RNA polymerase they contain, there is a further level of specialisation present. There are some factories that only transcribe a certain set of related genes, this further strengthens the concept that the main function of a transcription factory is for transcriptional efficiency.
Assembly and maintenance
There is much debate to whether transcription factories assemble because of the transcriptional demands of the genome or if they are stable structures that are conserved over time. Experimentally, it appears that they remain fixed over a short period of time; newly made mRNA were pulse labelled over 15 minutes and it showed no new transcription factories appearing. This is also supported by inhibition experiments. In these studies heat shock was used to turn off transcription which resulted in no change in the number of polymerases detected. It should be noted that upon further analysis of western blot data it was suggested that there was in fact a slight decrease over time of transcription factories. Therefore, it could be claimed that polymerase molecules are released gently over time from the factory when there is a lack of transcription which would eventually lead to the complete loss of the transcription factory.
There is also several pieces of evidence that promotes the idea of transcription factories assembling de novo due to transcriptional demands. GFP polymerase fluorescence experiments have shown that the inducement of transcription in Drosophila polytene nuclei leads to the formation of a factory which contradicts the notion of a stable and secure structure.
It was previously thought that it was the relatively small RNA polymerase that moves along the comparatively larger DNA template during transcription. However, increasing evidence supports the notion that due to the tethering of a transcription factory to the nuclear matrix, it is in fact the large DNA template that is moved to accommodate RNA polymerisation. In vitro studies for example have shown that RNA polymerases attached to a surface are capable of both rotating the DNA template and threading it through the polymerase to start transcription; which indicates the capabilities of RNA polymerase to be a molecular motor. Chromosome Conformation Capture (3C) also supports the idea of the DNA template diffusing towards a stationary RNA polymerase.
There remains a doubt to this mechanism of transcription. Firstly, it is unknown how a stationary polymerase is capable of transcribing genes on the (+)-strand and (-)-strand at the same genomic locus at the same time. This is in addition to a lack of conclusive evidence on how the polymerase remains immobilised (how it is tethered) and to what structure it is tethered to.
Effect on genomic and nuclear structure
There are several consequences the formation of a transcription factory has on nuclear and genomic structures. It has been proposed that the factories are responsible for nuclear organisation; they have been suggested to promote chromatin loop formation by two potential mechanisms:
The first mechanism suggests that loops form because 2 genes on the same chromosome require the same transcription machinery that would be found in a specific transcription factory. This requirement will attract the gene loci to the factory thus creating a loop.
The second mechanism suggests that chromatin loop formation is because of ‘depletion attraction’. This is a physical phenomenon that happens when a relatively large objects (such as a transcription factory) are in a populous area containing soluble objects (for example, proteins). The transcription factories tend to aggregate as their clustering prevents smaller objects from being a part of the region of overlap thus reducing the entropy of the system and therefore a chromatin loop would be produced between the 2 factories.
Transcription factories are also suggested to be responsible for gene clustering, this is because related genes would require the same transcriptional machinery and if a factory satisfies these needs the genes would be attracted to the factory . While the clustering of genes can be beneficial for transcriptional efficiency, there could be negative consequences to this. Gene translocation events occur when genes are in close proximity to one another; which will occur more often when a transcriptional factory is present. Gene translocation events, like point mutations, generally are detrimental to the organism and so therefore could lead to the possibility of disease. However, on the other hand recent research has suggested that there is no correlation between inter-gene interactions and translocation frequencies.
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