[noun] + 在于 + [noun / clause]
[noun] + 不在于 + [noun / clause],而在于 + [noun / clause]
在于 links a thing to what it lies in or turns on: the cause of a problem, the key to success, the difference between two things. The subject is usually an abstract noun – 问题, 关键, 原因, 区别, 意义 – and what follows can be a noun or a whole clause. It is a written, formal word.
The negative frame corrects a wrong idea of where the point lies: not here, but there. It is a fixture of essays and speeches.
With a decision or an outcome as the subject, 在于 means "is up to" or "depends on".
在于 already does the work of "is". Adding 是 doubles the verb.
In conversation 问题是… and 关键是… do the same job less formally.