The Bloom protein (BLM) and Topoisomerase IIIalpha are found in association with 
proteins of the Fanconi anemia (FA) pathway, a disorder manifesting increased 
cellular sensitivity to DNA crosslinking agents. In order to determine if the 
association reflects a functional interaction for the maintenance of genome 
stability, we have analyzed the effects of siRNA-mediated depletion of the 
proteins in human cells. Depletion of Topoisomerase IIIalpha or BLM leads to 
increased radial formation, as is seen in FA. BLM and Topoisomerase IIIalpha are 
epistatic to the FA pathway for suppression of radial formation in response to 
DNA interstrand crosslinks since depletion of either of them in FA cells does 
not increase radial formation. Depletion of Topoisomerase IIIalpha or BLM also 
causes an increase in sister chromatid exchanges, as is seen in Bloom syndrome 
cells. Human Fanconi anemia cells, however, do not demonstrate increased sister 
chromatid exchanges, separating this response from radial formation. Primary 
cell lines from mice defective in both Blm and Fancd2 have the same interstrand 
crosslink-induced genome instability as cells from mice deficient in the Fancd2 
protein alone. These observations demonstrate that the association of BLM and 
Topoisomerase IIIalpha with Fanconi proteins is a functional one, delineating a 
BLM-Topoisomerase IIIalpha-Fanconi pathway that is critical for suppression of 
chromosome radial formation.