Thanks for this. I didn't know about update-in. Are there other 'update' functions?
However, it's a good thing you want a DAG, because with immutable data structures you're hosed if you want a cyclic graph. Or at least you won't be building them out of such structures, which means you aren't getting to use Clojure's functions for sequences, collections and maps. Thus Clojure does not seem to be a good tool for graphs.