Common fragile sites have been involved in neoplastic transformation, although their molecular basis is still poorly understood. Here, we demonstrate that inhibition of the SMC1 by RNAi is sufficient to induce fragile site expression. By investigating normal, ATM- and ATR-deficient cell lines, we provide evidence that the contribution of SMC1 in preventing the collapse of stalled replication fork is an Atr-dependent pathway. Using a fluorescent antibody specific for gamma-H2AX, we show that very rare discrete nuclear foci appear 1 and 2 h after exposure to aphidicolin and/or RNAi-SMC1, but became more numerous and distinct after longer treatment times. In this context, fragile sites might be viewed as an in vitro phenomenon originating from double-strand breaks formed because of a stalled DNA replication that lasted too long to be managed by physiological rescue acting through the Atr/Smc1 axis. We propose that in vivo, following an extreme replication block, rare cells could escape checkpoint mechanisms and enter mitosis with a defect in genome assembly, eventually leading to neoplastic transformation.

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A simple and reliable statistical method is proposed to distinguish real fragile sites from the casual accumulation of aberrations that can occur as a consequence of random distribution. It is based on a study of the expected random distribution, assumed to be equal to a Poisson distribution, with the expected value of events per band as the mean.

Surface topography of human chromosomes was examined by atomic force microscopy during treatments for G-banding. Trypsin treatment resulted in a structural modification in the chromatin. Subsequent Giemsa staining caused a general swelling of the chromosomal surface that was greater in the areas of G-band positive regions. By means of a quantitative evaluation method we showed that the G-banding process produces a 10-fold enhancement of a pre-existing pattern of chromatin between G-band positive and G-band negative regions on mitotic chromosomes.

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