Astronomers have theorized
that the Big Bang governs the behavior of interstellar dust,
particles that comprise the atoms and molecules created in the progenitive explosion
and
persisting in even the emptiest regions of space.

The format of sentence is Main clause relative clause parallel modifiers.

Thus, only A makes the modifiers parallel (relative clause and participle modifier).

Looking at other options:

persists - This erroneously parallels to governs. Thus wrong.

persisted - past participle modifier particles changes the meaning of sentence (tense).

they persist - they is redundant and unnecessary.

are persisting - are not required.