If the raison d'etre of some piece of DNA is the regulation of neighboring pieces, then if it does so, that would constitute its expression, right? (We are nit-picking after all... Just ignore this.)
I can't really ignore this, it totally redefines the whole concept of gene expression. A gene is 'expressed' when it is transcribed as mRNA from its DNA template, and in canonical cases then translated into protein. To use 'expressed' in some other way is only going to confuse any familiar with molecular biology. You seem to be conflating gene expression and function.
Because they're good at causing themselves to be copied? Most "functional" genes use the complete organism as a means to get themselves copied and spread around. Maybe the CNEs are just hitching a ride? (Selfish gene talk, Dawkins and all that.)
Being copied is a distinct mechanism from being conserved. There are some 'junk' elements that lend themselves to increased copying, especially highly repetitive sequences where slippage can occur leading to duplications, but CNEs are usually identified from datasets where such repetitive elements have already been screened out. There still needs to be something acting to maintain the conserved sequence from simply degrading. These sequences are not like ERVs or other remnant proto-viral sequences which can sometimes proliferate through reinfection.
If this were merely a case of nearby sequences hitching a ride with selected genes then why do CNEs form islands of such high conservation, why aren't the other nearby sequences conserved?
The fact that we are identifying regulatory functions for CNEs suggests that what is going on is more directly relevant to organismal development/evolution than an artifact of genetic hitchhiking.
TTFN,
WK