Transcription factor proteins bound to DNA guarantee that cell expresses itself according to its differentiation. I have never asked myself what the mechanism of differentiation is (I should have a proper emoticon to describe this unpleasant feeling)! Transcription factors is it: they guarantee that correct genes are expressed.
As cell replicates the transcription factors disappear temporarily but are restored in mother and daughter cell later. How this happens looks like a complete mystery in the ordinary biochemistry in which one has soup of all kinds stupid molecules moving randomly around and making random collisions with similar idiots;-).
This problem is much more general and plagues all biochemistry. How just the correct randomly moving biomolecules of the dense molecular soup find each other - say say DNA and mRNA in transcription process and DNA and its conjugate in replication?
The TGD based answer is that reacting molecules are connected or get connected by rather long magnetic flux tubes, which actually appear as pairs (this is not relevant for the argument). Then magnetic flux tubes contract and force the reacting molecules close to each other. The contraction of the dark magnetic flux tube is induced by a reduction of Plankc constant heff=n×h: this does not occur spontaneously since one ends up to a higher criticality. This conclusions follows by accepting the association of a hierarchy of criticalities to a hierarchy of Planck constants and fractal hierarchy of symmetry breakings for what I call supersymplectic algebra possessing natural conformal structure and the hierarchy of isomorphic sub-algebras for which the conformal weights of the original algebra are multipled by integer n characterizing the sub-algebra. Metabolic energy would be needed at this stage.
As a matter fact, the general rule would be that anything requiring reduction of Planck constant demands metabolic energy. Life can be seen as an endless attempt to bet back to higher criticality and spontaneous drifting to lower criticality. Buddhists understood this long time ago and talked about Karma's law: the purpose of life is to keep heff low and fight with all means to avoid spiritual awakening;-). In biological death we have again the opportunity to get rid of this cycle and get enlightened. Personally I do not dare to be optimistic;-).
In the case of cell replication also the transcription factors replicate just as the DNA but stay farther away from DNA during the replication: the value of heff has spontaneously increased during replication period as it happens as conscious entity "dies";-). When the time is ripe, their heff is reduced and they return to their proper place near DNA and the fight with Karma's law continues again. Note that this shows also that death is not a real thing at molecular level. Same should be true at higher levels of fractal self hierarchy.