Early replication fragile sites: where replication-transcription collisions cause genetic instability.

Although it is known that replication stress causes genetic instability, the underlying mechanisms are not yet fully understood. A new study by Barlow et al (2013) used an elegant genome-wide chromatin immunoprecipitation approach to reveal that DNA lesions induced by replication stress occur predominantly in early replicating and actively transcribed gene clusters. These ‘early replication fragile sites’ (ERFS) can be the source for rearrangements commonly found in cancer, and represent a new type of fragile site, distinct from common fragile sites (CFS). Genetic instability is a threat to the integrity of DNA and underlies the genomic rearrangements that need to occur early in preneoplastic lesions in order to cause the genetic changes required for development into neoplastic disease. It has been demonstrated that cellular oncogenes, such as mos, cdc6, cyclin E and ras, not only provide proliferation signals but also induce replication stress associated with the formation of DNA double-strand breaks (DSBs). These DSBs lead to the activation of the ATM–p53 tumour barrier that prevents tumour growth, but can also drive genetic instability in cancer (Bartkova et al, 2006; Di Micco et al, 2006). Until now, it has been unclear how DNA damage arises in the context of replication stress. In a new study published in Cell (Barlow et al, 2013), Nussenzweig and co-workers employed chromatin immunoprecipitation with an anti-RPA antibody for genome-wide identification of ssDNA regions after inducing replication stress, which colocalise with newly replicated regions. This approach allowed mapping DNA regions associated with DNA damage. Interestingly, a high proportion of the damaged DNA regions were found within transcriptionally active gene clusters that replicate early. Furthermore, the same DNA regions were damaged both upon hydoxyureaand oncogene-induced replication stress, and their colocalisation with other DNA-damage response proteins (i.e., BRCA1 and SMC5) further indicated that they were repaired by homologous recombination. The damaged DNA regions caused by replication stress, termed ‘early replicating fragile sites’ (ERFS), are