FA2020 pg 612

HOX genes are implicated in segmental organization in cranial-caudal direction

transcription factor coding!!

mutations cause limb problems; isotretinoin leads to increased HOX expression

I think this is another prime example of NBME not expecting you to know every small detail but instead just answer their question straightforwardly. The question said "...involved in reproducible changes in HOX gene expression" and the only answer choice that deals with modifying gene expression is: transcription factors.