Figure 11: TSS shift as potential regulator of the eligibility of an mRNA for the amplification process.

Single line: 3’terminus of the antisense strand. Filled grey boxes: sense strand. Filled blue boxes: topologically compatible complementary elements on the antisense strand. A: one of the complementary elements is 3’-terminal; folding results in a self-priming structure that is extended into the sense strand. B: both complementary elements are internal, no self-priming is possible; TSS shift in the downstream direction makes one of the elements 3’-terminal and allows self-priming and extension into the sense strand. C: there are no complementary elements/no self-priming; TSS shift in the upstream direction generates 3’-terminal complementary element and thus enables self-priming and extension. Note that processes depicted in panels B and C can occur in reverse, resulting in a loss, rather than the acquisition, of the eligibility.