I have rooted Nexus 4 with Clockmod Recovery and there are always problems with OTA upgrades. After JWR66Y upgrade, which actually go smoothly. The problem is that SuperSU will be overwritten during upgrade and its not accessible anymore.
There is many articles in internet about this issue, but this one is really short description and it works :-). Another question - is rooting really needed, because it can be also security issue, but this is another story.
