After mixing the dough, our recipes only require two hours at room temperature for their initial rise (assuming you’ve used lukewarm water); then the container goes into the refrigerator where it can be stored for up to two weeks (depending on the recipe). According to the U.S. Department of Agriculture, the answer to this question depends on whether there were eggs in the recipe. Their website says that eggs should be refrigerated after two hours at room temperature (see their website, scroll down to relevant section).
For our doughs without eggs, when we’ve occasionally forgotten a batch and left it on the counter overnight, we’ve found that this has little effect on the final result, maybe just shortens the batch life by a day or two.
So, what would USDA recommend if you’re doing a long rise with dough containing eggs? Sounds like the first two hours are safe at room temperature, then into the refrigerator to complete the rising. We leave it to our readers to decide about how to handle egg doughs in light of USDA’s recommendation.