A method includes forming an isolation region extending into a semiconductor substrate, etching a top portion of the isolation region to form a recess in the isolation region, and forming a gate stack extending into the recess and overlapping a lower portion of the isolation region. A source region and a drain region are formed on opposite sides of the gate stack. The gate stack, the source region, and the drain region are parts of a Metal-Oxide-Semiconductor (MOS) device.