Model for integration of crRNAs into three distinct crRNP effector complexes. The CRISPR locus (repeat: black rectangles, invader-derived guide sequences: multiple colors) is transcribed from a promoter in the leader (brown) to form the pre-crRNA. Cas6 cleaves once in each repeat element of the pre-cRNA transcript to generate 1X RNA intermediates that each contain the 5′ tag, entire guide sequence, and 22 nt of 3′ repeat. Further 3′ end trimming by unknown mechanisms occurs either before, during, or after association with specific Cas proteins. The Cmr complex (blue) associates with two forms of crRNAs lacking any 3′ repeat. Csa (green) and Cst (yellow) complexes harbor crRNAs that contain variable amounts of 3′ repeat and one crRNA species without any 3′ repeat. Each crRNA size form can assemble into the corresponding effector complexes (one crRNA/complex) and guide targeting. The Cmr complex cleaves complementary RNA targets. The Csa and Cst effector complexes are predicted to target DNA homologous to the guide sequences in the crRNAs.
