What would be a single elegant-sounding word denoting controlled increase or decrease?
There's a reason why you encounter these words so frequently - they are widely understood, concise descriptions that almost any biologist will understand immediately. Almost any other terms you use in their place will only serve to obfuscate the actual biological phenomenon you're talking about.
That said, I've seen the words overexpressed and underexpressed to describe genes that are upregulated or downregulated, but they're not any less cumbersome words, nor are they used any more frequently outside the domain of biology. There are also may be some connotations about the cause of the effect, so there may be subtle differences between upregulation and overexpression depending on who you ask. I don't think there's any better terms than upregulation and downregulation for describing an effect of increased/decreased gene expression.