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.
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.