Reporter constructs work because we have been able to work out which elements present upstream of the
translation start site are required for expression of the
mRNA. Almost all of this knowledge was gained from analysing how viruses get their
genes expressed in the host
cell. They have had to evolve promoters that are short and strong enough to get enough of their
genes expressed to allow new progeny virions to form before the host organism "notices" and does something about it.
As most reporter constructs are only required transiently, the fact that the
cell does recognize them as foreign isn't too great a problem. However, scientists doing non-viral
gene therapy spend a lot of time modifying their nucleic acid based vectors so that they persist for as long as possible.