Why are some chromosomal regions particularly susceptible to breakage? Finding the answer to this question is crucial because this fragility is a factor in tumour development. A team from the Institute of Genetics and Molecular & Cellular Biology (CNRS/Inserm/University of Strasbourg) has just solved part of the mystery. Laszlo Tora and his colleagues have discovered that breakage in the longest human genes is caused by a phenomenon that, until now, was thought unlikely to occur in mammalian cells: interference between two key genetic processes, DNA transcription and replication. This research, published in the journalMolecular Cell on 23 December 2011, could eventually lead to novel strategies for fighting tumours.
Laszlo Tora and his team began by studying the transcription of very large human genes (more than 800 kilobases) that are known to exhibit DNA breaks called ‘common fragile sites’. They started out on the assumption that, as transcription of these very large genes takes an extremely long time, the transcription process could be a factor in the appearance of fragile sites.
Left: chromosomes with no breaks: the chromosomes are perfectly symmetrical. Right: chromosomes with breaks leading to chromosomal rearrangements.
The researchers used flow cytometry to put this assumption to the test. The use of this technology allowed them to sort cells according to the stage they had reached in the cell cycle  – cells in the G1 phase (gene transcription and cell growth), S phase (DNA replication), G2 phase (growth and preparation for cell division) and M phase (cell division). It emerged from this analysis that the transcription of very large genes took far longer than one cell cycle and was not completed until the beginning of the next cycle, in the G1 or S phase. This initial result is surprising for, until now, it had been assumed that gene transcription in mammals occurred within a single cell cycle, mostly during the G1 phase.
As replication takes place during the S phase, the research team suspected that breakage in very large mammalian genes could be due to interference between transcription and replication. They therefore focused on replication in these genes. It was found that replication in fragile site regions occurs at the end of the S phase, while transcription is still in progress in the same regions! This discovery has challenged current ideas in genetics. Until this study, it was generally believed that DNA transcription and replication complexes could not collide in mammals.
To explore this phenomenon further, the team then tried to discover what it was exactly that could weaken DNA in the event of replication and transcription collision. They discovered the presence of lasting loop structures caused by DNA hybridising with the RNA molecule produced during transcription. It is these DNA/RNA loops that would appear to destabilise DNA to such an extent as to cause breakage in the event of stress.
This crucial discovery opens up new prospects for medical research, for these loops can be seen as possible targets for reducing genomic instability and the development of tumours.
 Process through which DNA is copied into RNA. The RNA is then ‘translated’ into proteins to allow the cell to function.
 Process allowing DNA to split before cell division.
 DNA is measured in kilobases (1 kb = 1000 DNA base pairs).
 The four cell cycle phases: G1 (gene transcription and cell growth), S (DNA replication), G2 (growth and preparation for cell division) and M (division).
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