It indicates that the sentence is a question. Estne Corinna in urbe? Is Corinna in the city?
-ne indicates that it is a question. Without this it would be a statement: "the boys are at home"
Like the others said, it marks yes/no questions. Just adding a quick bit of background: Since word order in Latin is so fluid, simply moving the verb to the beginning of the sentence doesn't do the trick. Hence an extra marker. :)