No named character rules the Universe at the end of the Dune saga. There is a vast interstellar empire in Dune which rules thousands or millions of star systems.
But there are hundreds of billions of stars in our galaxy and hundreds of billions of galaxies in the observed part of the universe. Thus the Human space empire in Dune rules a tiny drop in the sea of space.
And the mightiest alien space emperor who might exist in the Dune universe unknown to the characters and the readers does not rule the universe, because he does not rule the Human Empire.
If the empire in Dune ruled the Universe, the highest nobles in Dune would not be dukes. There would be kings ruling kingdoms, subordinate to Kings of kings (kings to the second power) who would be subordinate to kings of kings of kings (kings to the third power) and on up to kings to the 47th power, kings to the 99th power, kings to the 457th power, kings to the 1,826th power and on up to THE EMPEROR.