MySql Server has gone away

I keep getting a run of this 2006 (Mysql server has gone away) error, around the same time in the small hours. Probably lasts for only 1 or 2 page hits.
Obviously traffic at this time of day is pretty low, so I thought it might be a cron job. But there’s nothing that runs at this time that isn’t running at other times during the day.
But the Server has started occasionally going away sporadically at other, more critical, times of the day too.
Any hints as to how I can investigate & fix the cause of this error?

This might happen if your mysql server is crashed. Me too faced this problem last week. Due to MySQL InnoDB engine is crashed, which is unrecoverable. So when i restart the MySQL service, then immediately accessing few pages will give error as “Mysql server has gone away”.
Check with your server support to identify is there any problem in MySQL.

If not then it is something to do with your code, may be it is not coded properly with MySQL connections.

Well it’s been happening pretty regularly in the early hours, and sorting itself out without intervention. I’ve had the server admins look at it and they can’t see anything to do with the actual server.
Code-wise, what kind of thing should I be looking for? Is there anything I could log that might show any scripts that could be causing this?