Fanconi anemia (FA) is characterized by cellular hypersensitivity to DNA 
crosslinking agents, but how the Fanconi pathway protects cells from DNA 
crosslinks and whether FA proteins act directly on crosslinks remain unclear. We 
developed a chromatin-IP-based strategy termed eChIP and detected association of 
multiple FA proteins with DNA crosslinks in vivo. Interdependence analyses 
revealed that crosslink-specific enrichment of various FA proteins is controlled 
by distinct mechanisms. BRCA-related FA proteins (BRCA2, FANCJ/BACH1, and 
FANCN/PALB2), but not FA core and I/D2 complexes, require replication for their 
crosslink association. FANCD2, but not FANCJ and FANCN, requires the FA core 
complex for its recruitment. FA core complex requires nucleotide excision repair 
proteins XPA and XPC for its association. Consistent with the distinct 
recruitment mechanism, recombination-independent crosslink repair was inversely 
affected in cells deficient of FANC-core versus BRCA-related FA proteins. Thus, 
FA proteins participate in distinct DNA damage response mechanisms governed by 
DNA replication status.