Meta-kernelization theorems are general results that provide polynomial kernels for large classes of parameterized problems. The known meta-kernelization theorems, in particular the results of Bodlaender et al. (FOCS'09) and of Fomin et al. (FOCS'10), apply to optimization problems parameterized by solution size. We present the first meta-kernelization theorems that use a structural parameters of the input and not the solution size. Let C be a graph class. We define the C-cover number of a graph to be a the smallest number of modules the vertex set can be partitioned into, such that each module induces a subgraph that belongs to the class C. We show that each graph problem that can be expressed in Monadic Second Order (MSO) logic has a polynomial kernel with a linear number of vertices when parameterized by the C-cover number for any fixed class C of bounded rank-width (or equivalently, of bounded clique-width, or bounded Boolean width). Many graph problems such as Independent Dominating Set, c-Coloring, and c-Domatic Number are covered by this meta-kernelization result. Our second result applies to MSO expressible optimization problems, such as Minimum Vertex Cover, Minimum Dominating Set, and Maximum Clique. We show that these problems admit a polynomial annotated kernel with a linear number of vertices.