Very quickly, you're absolutely right. There is a relatively new clause in the Russian criminal code that officially penalizes “separatist tendencies”.
If, for example, one of the Russian regions were to try to do what Putin did in Crimea in 2014, the so-called referendum, the people who would organize it would all be liable for criminal prosecution under current Russian law. And, yes, there are many people in the regions, including many representatives of Russia's indigenous ethnic groups, who are particularly prosecuted and persecuted.
I think it's also important to state that, in this sense at least, the Putin regime is an equal opportunities persecutor. If you look at the list of political prisoners in Russia, you will find representatives of many ethnic groups, many different religions, many different social walks of life. But of course still, just as in Stalin's time, numerically the largest group of them are the Russian people themselves.