I would go for option A.
'that' should be followed by 'tell'. We use a plural verb because:
Biologists believe that they have found one of the substances
that ________ quiescent in the earliest phases of an embryo's development.
The first half clearly states that there are more than one kind of such substances. Here we are talking about all such substances (out of which they have found one), so we use a plural verb 'tell'.
Options left A, B and E
(A) tell individual genes both when to become active and when to remain---- best
(B) tell individual genes both at which time they should become active and should remain
-----too wordy and incorrect grammar.
(E) tell an individual gene both about when it should become active and when it should remain
---use of about is incorrect and sentence is wordy.
"Always....Read between the lines"