By forming a trench isolation structure after providing a high-k dielectric layer stack, direct contact of oxygen-containing insulating material of a top surface of the trench isolation structure with the high-k dielectric material in shared polylines may be avoided. This technique is self-aligned, thereby enabling further device scaling without requiring very tight lithography tolerances. After forming the trench isolation structure, the desired electrical connection across the trench isolation structure may be re-established by providing a further conductive material.